Output of GX/GN in non-solo runs

[deto]

The release notes for 2.7.6 note that GX/GN can be output for all runs, however I just tried a run of the form:

/home/ubuntu/programs/STAR-2.7.8a/bin/Linux_x86_64/STAR \
    --outSAMtype BAM SortedByCoordinate \
    --outSAMunmapped Within \
    --outSAMattributes NH HI AS nM GX GN \
    --genomeDir /home/ubuntu/References/GRCh38_STAR \
    --readFilesIn path/to/my/reads \
    --quantMode GeneCounts \
    --runThreadN 16

And the resulting BAM file does not contain these. Is there an argument that I'm missing?

(The fixed was referenced in #945)

[alexdobin]

Hi David,

I was struggling with this issue for a few releases - could you please try 2.7.8a?

Cheers
Alex

[deto]

This was in 2.7.8a, actually

[alexdobin]

Hi David,

you are right, this is still not working. Will fix it shortly.
Note that GX/GN tags are assigned to STARsolo-like rules, i.e. the reads are required to be concordant with transcript models. On the other hand, the counts for --quantMode GeneCounts only require 1b overlap with exons.

Cheers
Alex

[cnk113]

I just want to add this doesn't seem to work with CB_samTagOut parameter set, although looking at the source code it looks like it was intended. Would it be possible to add the parameter to add the GX/GN tag w/o quantification? As well as allowing it with the GeneFull parameter?

[alexdobin]

Hi Chang,

GX/GN should now work for GeneFull in release 2.7.9, and even non-solo runs. I will check what's going on with CB_samTagOut.

Cheers
Alex

[cnk113]

I think the issue is in ParametersSolo.cpp line 218. I ended up removing the outer if statement and works for me.

STAR/source/ParametersSolo.cpp

Line 218 in ac39348

if (type != SoloTypes::CB_samTagOut) {//gene quantification is needed

[alexdobin]

Hi Chang,

you are right, removing this condition should make it work. I think there should be no issues, but I need to test it.

Cheers
Alex