stringtie(1)
assemble short RNAseq reads to transcripts
Description
STRINGTIE
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:
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--version : print just the version at stdout and exit | |
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--conservative : conservative transcript assembly, same as -t -c 1.5 -f 0.05 | |
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--mix : both short and long read data alignments are provided | |
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--rf : assume stranded library fr-firststrand | |
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--fr : assume stranded library fr-secondstrand | |
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-G reference annotation to use for guiding the assembly process (GTF/GFF3) | |
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--ptf : load point-features from a given 4 column feature file <f_tab> | |
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-o output path/file name for the assembled transcripts GTF (default: stdout) | |
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-l name prefix for output transcripts (default: STRG) | |
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-f minimum isoform fraction (default: 0.01) | |
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-L long reads processing; also enforces -s 1.5 -g 0 (default:false) | |
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-R if long reads are provided, just clean and collapse the reads but |
do not assemble
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-m minimum assembled transcript length (default: 200) |
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-a minimum anchor length for junctions (default: 10) |
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-j minimum junction coverage (default: 1) |
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-t disable trimming of predicted transcripts based on coverage |
(default: coverage trimming is enabled)
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-c minimum reads per bp coverage to consider for multi-exon transcript |
(default: 1)
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-s minimum reads per bp coverage to consider for single-exon transcript |
(default: 4.75)
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-v verbose (log bundle processing details) |
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-g maximum gap allowed between read mappings (default: 50) |
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-M fraction of bundle allowed to be covered by multi-hit reads (default:1) |
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-p number of threads (CPUs) to use (default: 1) |
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-A gene abundance estimation output file |
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-E define window around possibly erroneous splice sites from long reads to |
look out for correct splice sites (default: 25)
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-B enable output of Ballgown table files which will be created in the |
same directory as the output GTF (requires -G, -o recommended)
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-b enable output of Ballgown table files but these files will be |
created under the directory path given as <dir_path>
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-e only estimate the abundance of given reference transcripts (requires -G) | |
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--viral : only relevant for long reads from viral data where splice sites |
do not follow consensus (default:false)
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-x do not assemble any transcripts on the given reference sequence(s) |
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-u no multi-mapping correction (default: correction enabled) |
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-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)
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-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.