NAME

       stringtie - StringTie

DESCRIPTION

   StringTie v2.1.1 usage:
              stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]

              [-v]   [-a   <min_anchor_len>]   [-m   <min_tlen>]   [-j   <min_anchor_cov>]  [-f  <min_iso>]  [-C
              <coverage_file_name>] [-c <min_bundle_cov>] [-g  <bdist>]  [-u]  [-L]  [-e]  [-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
              transcriptome 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) -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
              use long reads settings (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

       -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)

       -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.