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Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to Thank you.


Successful execution of the StringTie1.3.3 will contain several files and directories:

  1. StringTie_output: all the default output files from the StringTie1.3.3 run
    1. sample1
      1. e2t.ctab:table with two columns, e_id and t_id, denoting which exons belong to which transcripts
      2. e_data.ctab:exon-level expression measurements
      3. i2t.ctab:table with two columns, i_id and t_id, denoting which introns belong to which transcripts
      4. i_data.ctab: intron- (i.e., junction-) level expression measurements. One row per intron. Columns are i_id (numeric intron id), chrstrandstartend (genomic location of the intron), and the following expression measurements for each sample
      5. t_data.ctab:transcript-level expression measurements. One row per transcript.
      6. abundances will be reported (tab delimited format) in the output file with the given name
      7.  sample1.gtf: Assembled transcript gtf file
      8. sample1.refs.gtf:StringTie outputs a file with the given name with all transcripts in the provided reference file that are fully covered by reads
  2. ballgown_input_files: Use this directory as input to StringTie-1.3.3_to_DESeq2_and_edegeR and Ballgown apps for differential expression analysis
    1. sample1: all *ctab files for sample1 and sample1.gtf
    2. sample2: all *ctab files for sample2 and sample2.gtf
  3. gtf_files: all transcript assembly files: Use this directory for StringTie-1.3.3_merge app
    1. sample1.gtf
    2. sample2.gtf

More information on the tool can be found here -