2nd Pass Alignment with STAR for RNA-sequencing

[cbaudo]

Hello everyone,

Firstly, thanks for reading this post. I'm performing 2nd pass alignment with STAR and I was wondering how to merge SJ.out.tab files. I'll be performing the first phase alignment on ~21 files and will need to merge 21 SJ.out.tab files. I couldn't find an explanation in the manual on how to merge these files prior to creating a new genome index for the second pass.

I appreciate your time,
cbaudo

[mmackattack]

I'm also having trouble with this concept.

[LeonDK]

Hopefully your directory structure is setup in such a way, that you can do something along the lines of:

cat /path/to/my/project/results/alignments/mySample*/SJ.out.tab >/path/to/desired/output/directory/all.SJ.out.tab

Where the asterix could be e.g.: 01,02,...,21

Cheers,
Leon

[cbaudo]

Many thanks, Leon.