StringTie-Teaching - Revision history

Shtsai at 01:36, 5 April 2026

2026-04-05T01:36:05Z

← Older revision		Revision as of 21:36, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==
	2.2.3, 3.0.0		2.2.3, 3.0.0

	=== Author / Distributor ===		== Author / Distributor ==

	[http://ccb.jhu.edu/software/stringtie/ StringTie]		[http://ccb.jhu.edu/software/stringtie/ StringTie]

	=== Description ===		== Description ==
	"StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts."		"StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts."
	More details are at [http://ccb.jhu.edu/software/stringtie/ StringTie]		More details are at [http://ccb.jhu.edu/software/stringtie/ StringTie]

	=== Running Program ===		== Running Program ==

	'''Version 2.2.3'''		'''Version 2.2.3'''
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from [http://ccb.jhu.edu/software/stringtie/ StringTie]		Source code is obtained from [http://ccb.jhu.edu/software/stringtie/ StringTie]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 20:51, 9 January 2026

2026-01-09T20:51:56Z

← Older revision		Revision as of 16:51, 9 January 2026
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	=== Version ===		=== Version ===
	2.2.1		2.2.3, 3.0.0

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	Version 2.2.~~1 of this application~~ is in /apps/eb/StringTie/2.2.1-GCC-~~11.2.0 or /apps/eb/StringTie/2.2.1-GCC-11~~.3.0		'''Version 2.2.3'''
			It is installed in /apps/eb/StringTie/2.2.3-GCC-12.3.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/2.2.1-GCC-11.2.0		ml StringTie/2.2.3-GCC-12.3.0
			</pre>

			'''Version 3.0.0'''
			It is installed in /apps/eb/StringTie/3.0.0-GCC-13.3.0

			To use this version, please load the module with
			<pre class="gscript">
			ml StringTie/3.0.0-GCC-13.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/2.2.1-GCC-11.2.0<br>		ml StringTie/3.0.0-GCC-13.3.0<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/2.2.1-GCC-11.2.0		ml StringTie/3.0.0-GCC-13.3.0

	stringtie --help		stringtie --help
			StringTie v3.0.0 usage:
	StringTie v2.2.1 usage:

	stringtie <in.bam ..> [-G <guide_gff>] [-l <prefix>] [-o <out.gtf>] [-p <cpus>]		stringtie <in.bam ..> [-G <guide_gff>] [-l <prefix>] [-o <out.gtf>] [-p <cpus>]
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	-p number of threads (CPUs) to use (default: 1)		-p number of threads (CPUs) to use (default: 1)
	-A gene abundance estimation output file		-A gene abundance estimation output file
			-N : use with non-polyA RNA-seq
			--nasc : output nascent transcripts
	-E define window around possibly erroneous splice sites from long reads to		-E define window around possibly erroneous splice sites from long reads to
	look out for correct splice sites (default: 25)		look out for correct splice sites (default: 25)
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	created under the directory path given as <dir_path>		created under the directory path given as <dir_path>
	-e only estimate the abundance of given reference transcripts (requires -G)		-e only estimate the abundance of given reference transcripts (requires -G)
	--viral : only relevant for long reads from viral data where splice sites		--viral only relevant for long reads from viral data where splice sites
	do not follow consensus (default:false)		do not follow consensus (default:false)
	-x do not assemble any transcripts on the given reference sequence(s)		-x do not assemble any transcripts on the given reference sequence(s)

Chelsea: /* Running Program */

2024-05-14T13:37:20Z

Running Program

← Older revision		Revision as of 09:37, 14 May 2024
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	=== Running Program ===		=== Running Program ===

	Version 2.2.1 of this application is in /apps/eb/StringTie/2.2.1-GCC-11.2.0		Version 2.2.1 of this application is in /apps/eb/StringTie/2.2.1-GCC-11.2.0 or /apps/eb/StringTie/2.2.1-GCC-11.3.0

	To use this version, please load the module with		To use this version, please load the module with

Shtsai at 18:00, 6 September 2023

2023-09-06T18:00:37Z

← Older revision		Revision as of 14:00, 6 September 2023
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	=== Version ===		=== Version ===
	2.1.1		2.2.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	Version 2.1.1 of this application is in /apps/eb/StringTie/2.1.1-GCC-8.3.0		Version 2.2.1 of this application is in /apps/eb/StringTie/2.2.1-GCC-11.2.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/2.1.1-GCC-8.3.0		ml StringTie/2.2.1-GCC-11.2.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/2.1.1-GCC-8.3.0<br>		ml StringTie/2.2.1-GCC-11.2.0<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/2.1.1-GCC-8.3.0		ml StringTie/2.2.1-GCC-11.2.0

	stringtie --help		stringtie --help
	StringTie v2.1.1 usage:
	stringtie <~~input~~.bam ..> [-G <guide_gff>] [-l <~~label~~>] [-o <~~out_gtf~~>] [-p <cpus>]		StringTie v2.2.1 usage:
	[-v] [-a <min_anchor_len>] [-m <~~min_tlen~~>] [-j <min_anchor_cov>] [-f <min_iso>]
	~~[-C <coverage_file_name>]~~ [-c <min_bundle_cov>] [-g <bdist>] [-u] [-L]		stringtie <in.bam ..> [-G <guide_gff>] [-l <prefix>] [-o <out.gtf>] [-p <cpus>]
	[-e] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B \| -b <dir_path>}		[-v] [-a <min_anchor_len>] [-m <min_len>] [-j <min_anchor_cov>] [-f <min_iso>]
			[-c <min_bundle_cov>] [-g <bdist>] [-u] [-L] [-e] [--viral] [-E <err_margin>]
			[--ptf <f_tab>] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B\|-b <dir_path>}
			[--mix] [--conservative] [--rf] [--fr]
	Assemble RNA-Seq alignments into potential transcripts.		Assemble RNA-Seq alignments into potential transcripts.
	Options:		Options:
	--version : print just the version at stdout and exit		--version : print just the version at stdout and exit
	--conservative : conservative ~~transcriptome~~ assembly, same as -t -c 1.5 -f 0.05		--conservative : conservative transcript assembly, same as -t -c 1.5 -f 0.05
	--rf assume stranded library fr-firststrand		--mix : both short and long read data alignments are provided
	--fr assume stranded library fr-secondstrand		(long read alignments must be the 2nd BAM/CRAM input file)
	-G reference annotation to use for guiding the assembly process (GTF/~~GFF3~~)		--rf : assume stranded library fr-firststrand
			--fr : assume stranded library fr-secondstrand
			-G reference annotation to use for guiding the assembly process (GTF/GFF)
			--ptf : load point-features from a given 4 column feature file <f_tab>
	-o output path/file name for the assembled transcripts GTF (default: stdout)		-o output path/file name for the assembled transcripts GTF (default: stdout)
	-l name prefix for output transcripts (default: STRG)		-l name prefix for output transcripts (default: STRG)
	-f minimum isoform fraction (default: 0.01)		-f minimum isoform fraction (default: 0.01)
	-L ~~use~~ long reads ~~settings~~ (default:false)		-L long reads processing; also enforces -s 1.5 -g 0 (default:false)
	-R if long reads are provided, just clean and collapse the reads but do not assemble		-R if long reads are provided, just clean and collapse the reads but
			do not assemble
	-m minimum assembled transcript length (default: 200)		-m minimum assembled transcript length (default: 200)
	-a minimum anchor length for junctions (default: 10)		-a minimum anchor length for junctions (default: 10)
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	-p number of threads (CPUs) to use (default: 1)		-p number of threads (CPUs) to use (default: 1)
	-A gene abundance estimation output file		-A gene abundance estimation output file
			-E define window around possibly erroneous splice sites from long reads to
			look out for correct splice sites (default: 25)
	-B enable output of Ballgown table files which will be created in the		-B enable output of Ballgown table files which will be created in the
	same directory as the output GTF (requires -G, -o recommended)		same directory as the output GTF (requires -G, -o recommended)
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	created under the directory path given as <dir_path>		created under the directory path given as <dir_path>
	-e only estimate the abundance of given reference transcripts (requires -G)		-e only estimate the abundance of given reference transcripts (requires -G)
			--viral : only relevant for long reads from viral data where splice sites
			do not follow consensus (default:false)
	-x do not assemble any transcripts on the given reference sequence(s)		-x do not assemble any transcripts on the given reference sequence(s)
	-u no multi-mapping correction (default: correction enabled)		-u no multi-mapping correction (default: correction enabled)
	-h print this usage message and exit		-h print this usage message and exit
			--ref/--cram-ref reference genome FASTA file for CRAM input

	Transcript merge usage mode:		Transcript merge usage mode:

Shtsai at 02:13, 28 August 2020

2020-08-28T02:13:31Z

← Older revision		Revision as of 22:13, 27 August 2020
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	=== Version ===		=== Version ===
	1.~~3.4d~~		2.1.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	~~The last version~~ of this application is ~~at /usr/local~~/apps/eb/StringTie/1.3.~~4d-foss-2016b~~		Version 2.1.1 of this application is in /apps/eb/StringTie/2.1.1-GCC-8.3.0

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/1.3.~~4d-foss-2016b~~		ml StringTie/2.1.1-GCC-8.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/1.3.~~4d-foss-2016b~~<br>		ml StringTie/2.1.1-GCC-8.3.0<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/1.3.~~4d-foss-2016b~~		ml StringTie/2.1.1-GCC-8.3.0

	stringtie --help		stringtie --help
	StringTie v1.3.4d usage:		StringTie v2.1.1 usage:
	stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]		stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
	[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]		[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]
	[-C <coverage_file_name>] [-c <min_bundle_cov>] [-g <bdist>] [-u]		[-C <coverage_file_name>] [-c <min_bundle_cov>] [-g <bdist>] [-u] [-L]
	[-e] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B \| -b <dir_path>}		[-e] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B \| -b <dir_path>}
	Assemble RNA-Seq alignments into potential transcripts.		Assemble RNA-Seq alignments into potential transcripts.
	Options:		Options:
	--version : print just the version at stdout and exit		--version : print just the version at stdout and exit
	-~~G reference annotation to use for guiding the~~ assembly ~~process (GTF/GFF3)~~		--conservative : conservative transcriptome assembly, same as -t -c 1.5 -f 0.05
	--rf assume stranded library fr-firststrand		--rf assume stranded library fr-firststrand
	--fr assume stranded library fr-secondstrand		--fr assume stranded library fr-secondstrand
			-G reference annotation to use for guiding the assembly process (GTF/GFF3)
			-o output path/file name for the assembled transcripts GTF (default: stdout)
	-l name prefix for output transcripts (default: STRG)		-l name prefix for output transcripts (default: STRG)
	-f minimum isoform fraction (default: 0.1)		-f minimum isoform fraction (default: 0.01)
			-L use long reads settings (default:false)
			-R if long reads are provided, just clean and collapse the reads but do not assemble
	-m minimum assembled transcript length (default: 200)		-m minimum assembled transcript length (default: 200)
	~~-o output path/file name for the assembled transcripts GTF (default: stdout)~~
	-a minimum anchor length for junctions (default: 10)		-a minimum anchor length for junctions (default: 10)
	-j minimum junction coverage (default: 1)		-j minimum junction coverage (default: 1)
	-t disable trimming of predicted transcripts based on coverage		-t disable trimming of predicted transcripts based on coverage
	(default: coverage trimming is enabled)		(default: coverage trimming is enabled)
	-c minimum reads per bp coverage to consider for transcript ~~assembly~~		-c minimum reads per bp coverage to consider for multi-exon transcript
	(default: 2.5)		(default: 1)
			-s minimum reads per bp coverage to consider for single-exon transcript
			(default: 4.75)
	-v verbose (log bundle processing details)		-v verbose (log bundle processing details)
	-g gap between read mappings ~~triggering a new bundle~~ (default: 50)		-g maximum gap allowed between read mappings (default: 50)
	~~-C output a file with reference transcripts that are covered by reads~~		-M fraction of bundle allowed to be covered by multi-hit reads (default:1)
	-M fraction of bundle allowed to be covered by multi-hit reads (default:~~0.95~~)
	-p number of threads (CPUs) to use (default: 1)		-p number of threads (CPUs) to use (default: 1)
	-A gene abundance estimation output file		-A gene abundance estimation output file

Yhuang at 19:47, 15 August 2018

2018-08-15T19:47:14Z

← Older revision		Revision as of 15:47, 15 August 2018
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	=== Version ===		=== Version ===
	1.3.3		1.3.4d

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/StringTie/1.3.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/StringTie/1.3.4d-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/1.3.3-foss-2016b		ml StringTie/1.3.4d-foss-2016b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/1.3.3-foss-2016b<br>		ml StringTie/1.3.4d-foss-2016b<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/1.3.3-foss-2016b		ml StringTie/1.3.4d-foss-2016b
	stringtie --help		stringtie --help
	StringTie v1.3.3 usage:		StringTie v1.3.4d usage:
	stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]		stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
	[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]		[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]

Yhuang at 19:47, 15 August 2018

2018-08-15T19:47:06Z

← Older revision		Revision as of 15:47, 15 August 2018
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	=== Version ===		=== Version ===
	1.3.4d		1.3.3

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/StringTie/1.3.4d-foss-2016b		The last version of this application is at /usr/local/apps/eb/StringTie/1.3.3-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/1.3.4d-foss-2016b		ml StringTie/1.3.3-foss-2016b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/1.3.4d-foss-2016b<br>		ml StringTie/1.3.3-foss-2016b<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/1.3.4d-foss-2016b		ml StringTie/1.3.3-foss-2016b
	stringtie --help		stringtie --help
	StringTie v1.3.4d usage:		StringTie v1.3.3 usage:
	stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]		stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
	[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]		[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]

Yhuang at 19:29, 15 August 2018

2018-08-15T19:29:04Z

← Older revision		Revision as of 15:29, 15 August 2018
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	=== Version ===		=== Version ===
	1.3.3		1.3.4d

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/StringTie/1.3.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/StringTie/1.3.4d-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/1.3.3-foss-2016b		ml StringTie/1.3.4d-foss-2016b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/1.3.3-foss-2016b<br>		ml StringTie/1.3.4d-foss-2016b<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/1.3.3-foss-2016b		ml StringTie/1.3.4d-foss-2016b
	stringtie --help		stringtie --help
	StringTie v1.3.3 usage:		StringTie v1.3.4d usage:
	stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]		stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
	[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]		[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]

Yhuang at 19:28, 15 August 2018

2018-08-15T19:28:57Z

← Older revision		Revision as of 15:28, 15 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	1.3.4d		1.3.3

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/StringTie/1.3.4d-foss-2016b		The last version of this application is at /usr/local/apps/eb/StringTie/1.3.3-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/1.3.4d-foss-2016b		ml StringTie/1.3.3-foss-2016b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/1.3.4d-foss-2016b<br>		ml StringTie/1.3.3-foss-2016b<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/1.3.4d-foss-2016b		ml StringTie/1.3.3-foss-2016b
	stringtie --help		stringtie --help
	StringTie v1.3.4d usage:		StringTie v1.3.3 usage:
	stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]		stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
	[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]		[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]

Yhuang at 16:26, 15 August 2018

2018-08-15T16:26:22Z

← Older revision		Revision as of 12:26, 15 August 2018
Line 9:		Line 9:

	=== Version ===		=== Version ===
	1.3.3		1.3.4d

	=== Author / Distributor ===		=== Author / Distributor ===
Line 21:		Line 21:
	=== Running Program ===		=== Running Program ===

	The last version of this application is at /usr/local/apps/eb/StringTie/1.3.3-foss-2016b		The last version of this application is at /usr/local/apps/eb/StringTie/1.3.4d-foss-2016b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml StringTie/1.3.3-foss-2016b		ml StringTie/1.3.4d-foss-2016b
	</pre>		</pre>

Line 43:		Line 43:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml StringTie/1.3.3-foss-2016b<br>		ml StringTie/1.3.4d-foss-2016b<br>
	stringtie <u>[options]</u><br>		stringtie <u>[options]</u><br>
	</div>		</div>
Line 59:		Line 59:

	<pre class="gcommand">		<pre class="gcommand">
	ml StringTie/1.3.3-foss-2016b		ml StringTie/1.3.4d-foss-2016b
	stringtie --help		stringtie --help
	StringTie v1.3.3 usage:		StringTie v1.3.4d usage:
	stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]		stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
	[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]		[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]