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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH STRINGTIE "1" "June 2021" "stringtie 2.1.6+ds" "User Commands"
.SH NAME
stringtie \- assemble short RNAseq reads to transcripts
.SH DESCRIPTION
StringTie v2.1.6 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>}
[\-\-mix] [\-\-conservative] [\-\-rf] [\-\-fr]
.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\-\-mix\fR : both short and long read data alignments are provided
.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)
.PP
Error: no input file provided!
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
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