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Columns in tabular overview of reads per gene after RNA STAR in Galaxy

Dear all,

I used RNA STAR from Galaxy and got 5 files.

  1. BAM
  2. BAI
  3. Log
  4. Splice junctions
  5. Reads per gene

The reads per gene file contains 4 columns, but they dont have any annotations.

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What is the difference among the last 3 columns?

Thank you in advance, Anton

rna-seq galaxy rna star alignment

1 answer

https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf

STAR outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options: column 1: gene ID column 2: counts for unstranded RNA-seq column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes) column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

Thank you very much.

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