.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH STRINGTIE "1" "November 2020" "stringtie 2.1.4" "User Commands"
.SH NAME
stringtie \- StringTie
.SH DESCRIPTION
StringTie v2.1.4 usage:
.PP
stringtie <in.bam ..> [\-G <guide_gff>] [\-l <prefix>] [\-o <out.gtf>] [\-p <cpus>]
.IP
[\-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>}
.PP
Assemble RNA\-Seq alignments into potential transcripts.
Options:
.HP
\fB\-\-version\fR : print just the version at stdout and exit
.HP
\fB\-\-conservative\fR : conservative transcript assembly, same as \fB\-t\fR \fB\-c\fR 1.5 \fB\-f\fR 0.05
.HP
\fB\-\-rf\fR : assume stranded library fr\-firststrand
.HP
\fB\-\-fr\fR : assume stranded library fr\-secondstrand
.HP
\fB\-G\fR reference annotation to use for guiding the assembly process (GTF/GFF3)
.HP
\fB\-\-ptf\fR : load point\-features from a given 4 column feature file <f_tab>
.HP
\fB\-o\fR output path/file name for the assembled transcripts GTF (default: stdout)
.HP
\fB\-l\fR name prefix for output transcripts (default: STRG)
.HP
\fB\-f\fR minimum isoform fraction (default: 0.01)
.HP
\fB\-L\fR long reads processing; also enforces \fB\-s\fR 1.5 \fB\-g\fR 0 (default:false)
.HP
\fB\-R\fR if long reads are provided, just clean and collapse the reads but
.IP
do not assemble
.HP
\fB\-m\fR minimum assembled transcript length (default: 200)
.HP
\fB\-a\fR minimum anchor length for junctions (default: 10)
.HP
\fB\-j\fR minimum junction coverage (default: 1)
.HP
\fB\-t\fR disable trimming of predicted transcripts based on coverage
.IP
(default: coverage trimming is enabled)
.HP
\fB\-c\fR minimum reads per bp coverage to consider for multi\-exon transcript
.IP
(default: 1)
.HP
\fB\-s\fR minimum reads per bp coverage to consider for single\-exon transcript
.IP
(default: 4.75)
.HP
\fB\-v\fR verbose (log bundle processing details)
.HP
\fB\-g\fR maximum gap allowed between read mappings (default: 50)
.HP
\fB\-M\fR fraction of bundle allowed to be covered by multi\-hit reads (default:1)
.HP
\fB\-p\fR number of threads (CPUs) to use (default: 1)
.HP
\fB\-A\fR gene abundance estimation output file
.HP
\fB\-E\fR define window around possibly erroneous splice sites from long reads to
.IP
look out for correct splice sites (default: 25)
.HP
\fB\-B\fR enable output of Ballgown table files which will be created in the
.IP
same directory as the output GTF (requires \fB\-G\fR, \fB\-o\fR recommended)
.HP
\fB\-b\fR enable output of Ballgown table files but these files will be
.IP
created under the directory path given as <dir_path>
.HP
\fB\-e\fR only estimate the abundance of given reference transcripts (requires \fB\-G\fR)
.HP
\fB\-\-viral\fR : only relevant for long reads from viral data where splice sites
.IP
do not follow consensus (default:false)
.HP
\fB\-x\fR do not assemble any transcripts on the given reference sequence(s)
.HP
\fB\-u\fR no multi\-mapping correction (default: correction enabled)
.HP
\fB\-h\fR print this usage message and exit
.SS "Transcript merge usage mode:"
.IP
stringtie \fB\-\-merge\fR [Options] { gtf_list | strg1.gtf ...}
.PP
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:
.TP
\fB\-G\fR <guide_gff>
reference annotation to include in the merging (GTF/GFF3)
.TP
\fB\-o\fR <out_gtf>
output file name for the merged transcripts GTF
(default: stdout)
.TP
\fB\-m\fR <min_len>
minimum input transcript length to include in the merge
(default: 50)
.TP
\fB\-c\fR <min_cov>
minimum input transcript coverage to include in the merge
(default: 0)
.TP
\fB\-F\fR <min_fpkm>
minimum input transcript FPKM to include in the merge
(default: 1.0)
.TP
\fB\-T\fR <min_tpm>
minimum input transcript TPM to include in the merge
(default: 1.0)
.TP
\fB\-f\fR <min_iso>
minimum isoform fraction (default: 0.01)
.TP
\fB\-g\fR <gap_len>
gap between transcripts to merge together (default: 250)
.TP
\fB\-i\fR
keep merged transcripts with retained introns; by default
these are not kept unless there is strong evidence for them
.TP
\fB\-l\fR <label>
name prefix for output transcripts (default: MSTRG)
.SH "SEE ALSO"
The full documentation for
.B stringtie
is maintained as a Texinfo manual.  If the
.B info
and
.B stringtie
programs are properly installed at your site, the command
.IP
.B info stringtie
.PP
should give you access to the complete manual.