Hello,
I'm new in the community but I found many helpful posts in the past, so here is my question.
I downloaded around 60 .bam files from the ENCODE repository. The header size was giving problems and I converted them to .sam as one of the answers in these thread suggested.
And when I run Cufflinks I get many lines with this error:
SAM error on line 862765: found spliced alignment without XS attribute
I am executing this on batch, so it is still running and, for some files, Cufflinks finish and produces the gene count, for other files I am not sure if it just hasn't finished yet.
I've been reading many posts about the XS attribute, but I don't know why would it be missing if I just converted from .bam to .sam. And would you know if it affects the read counts for genes?
Thank you,
Julia
I'm new in the community but I found many helpful posts in the past, so here is my question.
I downloaded around 60 .bam files from the ENCODE repository. The header size was giving problems and I converted them to .sam as one of the answers in these thread suggested.
Code:
samtools view -h -o file.sam file.bam
SAM error on line 862765: found spliced alignment without XS attribute
I am executing this on batch, so it is still running and, for some files, Cufflinks finish and produces the gene count, for other files I am not sure if it just hasn't finished yet.
I've been reading many posts about the XS attribute, but I don't know why would it be missing if I just converted from .bam to .sam. And would you know if it affects the read counts for genes?
Thank you,
Julia
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