Hi,
I had some troubles running Cufflinks with input mapping from HIsat2 (sam/bam).
Cufflinks man page says that input file should be sorted and contain XS tags. To add the tags, I specified --dta-cufflinks as parameter in for the alignment, following Hisat2 man page. With this parameter, supposedly, " [...] HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.". However, this tag does not appear in every line (read) of the generated bam file.
Is this possible and/or expectable? If you ever encountered this issue before, how could you fix it?
I was thinking to first generate a file like this prior to launch of Cufflinks run:
What do you think?
I had some troubles running Cufflinks with input mapping from HIsat2 (sam/bam).
Cufflinks man page says that input file should be sorted and contain XS tags. To add the tags, I specified --dta-cufflinks as parameter in for the alignment, following Hisat2 man page. With this parameter, supposedly, " [...] HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.". However, this tag does not appear in every line (read) of the generated bam file.
Is this possible and/or expectable? If you ever encountered this issue before, how could you fix it?
I was thinking to first generate a file like this prior to launch of Cufflinks run:
Code:
samtools view hisat2.sorted.bam | egrep 'XS:A:-|XS:A:+' > XS-Tagged.sorted.sam
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