stringtie - assemble short RNAseq reads to transcripts

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

stringtie 2.1.6+ds                                  June 2021                                       STRINGTIE(1)

       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:

       --version : print just the version at stdout and exit

       --conservative : conservative transcript assembly, same as -t-c 1.5 -f 0.05

       --mix : both short and long read data alignments are provided

       --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

   Transcriptmergeusagemode:
              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)

       Error: no input file provided!

       stringtie - assemble short RNAseq reads to transcripts