Page Comparison

...

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), chr, strand, start, end (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. sample1.abund.tab:Gene 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 - https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual

...