---
name: "stringtie"
section: "1"
platform: "linux"
package: "stringtie"
version: "2.2.1+ds-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/stringtie"
---

# stringtie(1)

assemble short RNAseq reads to transcripts

## NAME

stringtie - assemble short RNAseq reads to transcripts

## DESCRIPTION

StringTie v2.1.6 usage:

stringtie \<in.bam ..\> \[-G \<guide\_gff\>\] \[-l \<prefix\>\] \[-o \<out.gtf\>\] \[-p \<cpus\>\]

-

  \[-v\] \[-a \<min\_anchor\_len\>\] \[-m \<min\_len\>\] \[-j \<min\_anchor\_cov\>\] \[-f \<min\_iso\>\] \[-c \<min\_bundle\_cov\>\] \[-g \<bdist\>\] \[-u\] \[-L\] \[-e\] \[--viral\] \[-E \<err\_margin\>\] \[--ptf \<f\_tab\>\] \[-x \<seqid,..\>\] \[-A \<gene\_abund.out\>\] \[-h\] {-B\|-b \<dir\_path\>} \[--mix\] \[--conservative\] \[--rf\] \[--fr\]

Assemble RNA-Seq alignments into potential transcripts. Options:

**--version** : print just the version at stdout and exit

**--conservative** : conservative transcript assembly, same as **-t** **-c** 1.5 **-f** 0.05

**--mix** : both short and long read data alignments are provided

**--rf** : assume stranded library fr-firststrand

**--fr** : assume stranded library fr-secondstrand

**-G** reference annotation to use for guiding the assembly process (GTF/GFF3)

**--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)

**-l** name prefix for output transcripts (default: STRG)

**-f** minimum isoform fraction (default: 0.01)

**-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

**-m** minimum assembled transcript length (default: 200)

**-a** minimum anchor length for junctions (default: 10)

**-j** minimum junction coverage (default: 1)

**-t** disable trimming of predicted transcripts based on coverage

-

  (default: coverage trimming is enabled)

**-c** minimum reads per bp coverage to consider for multi-exon transcript

-

  (default: 1)

**-s** minimum reads per bp coverage to consider for single-exon transcript

-

  (default: 4.75)

**-v** verbose (log bundle processing details)

**-g** maximum gap allowed between read mappings (default: 50)

**-M** fraction of bundle allowed to be covered by multi-hit reads (default:1)

**-p** number of threads (CPUs) to use (default: 1)

**-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

-

  same directory as the output GTF (requires **-G**, **-o** recommended)

**-b** enable output of Ballgown table files but these files will be

-

  created under the directory path given as \<dir\_path\>

**-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)

**-u** no multi-mapping correction (default: correction enabled)

**-h** print this usage message and exit

### Transcript merge usage mode:

-

  stringtie **--merge** \[Options\] { gtf\_list \| strg1.gtf ...}

With this option StringTie will assemble transcripts from multiple input files generating a unified non-redundant set of isoforms. In this mode the following options are available:

- **-G** \<guide\_gff\>

  reference annotation to include in the merging (GTF/GFF3)

- **-o** \<out\_gtf\>

  output file name for the merged transcripts GTF (default: stdout)

- **-m** \<min\_len\>

  minimum input transcript length to include in the merge (default: 50)

- **-c** \<min\_cov\>

  minimum input transcript coverage to include in the merge (default: 0)

- **-F** \<min\_fpkm\>

  minimum input transcript FPKM to include in the merge (default: 1.0)

- **-T** \<min\_tpm\>

  minimum input transcript TPM to include in the merge (default: 1.0)

- **-f** \<min\_iso\>

  minimum isoform fraction (default: 0.01)

- **-g** \<gap\_len\>

  gap between transcripts to merge together (default: 250)

- **-i**

  keep merged transcripts with retained introns; by default these are not kept unless there is strong evidence for them

- **-l** \<label\>

  name prefix for output transcripts (default: MSTRG)

Error: no input file provided!

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.