Is there a manual to understand STAR output files?

Question

[ev97]

I am quite new in RNA-seq and I need to ask you if someone knows how can I find a web page, manual or something where I can see an explanation of all the output files that STAR gives.

I tried to solve my doubts in the STAR manual, but it only has the explanation for the "log files" >> log.out, log.progress.out and log.final.out.

I would like to understand the other files but I don't know how. For example, in the first step when you generate the indexes, STAR gives you all these files. Some of them are easy to understand by context and by their names.. but others, I would like to have an explanation, what information contains each column...

• chrLength.txt
• chrNameLength.txt
• chrName.txt
• chrStart.txt
• exonGeTrInfo.tab
• exonInfo.tab
• geneInfo.tab
• Genome
• genomeParameters.txt
• SA
• etc.

Thanks in advance,

Regards

[Ram]

I wouldn't really call these "output" files. They are the genome library files STAR uses to create its actual output files from alignment operations. As long as STAR's manual talks about those files, it doesn't need to explain the files it uses for its internal workings.

[ev97]

Thanks very much for your reply. I thought that I should understand all the files and I was worried because I couldn't find anything...

Answer 1

[Pierre Lindenbaum]

I would like to have an explanation, what information contains each column...

those files are internal/private to STAR, you don't have to understand them. You can always have a look at the code. For example: https://github.com/alexdobin/STAR/blob/ffb66fb04e2642d1c2df87a31344552487ec491d/source/GTF_transcriptGeneSJ.cpp#L47

[ev97]

Thanks very much for your reply, I am quite calm right now.