STRINGTIE(1)

NAME
stringtie - StringTie

DESCRIPTION
StringTie v2.1.4 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>}

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

--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)

SEE ALSO
The full documentation for stringtie is maintained as a Texinfo manual. If the info and stringtie programs are properly installed at your site, the command

    info stringtie

should give you access to the complete manual.