Dear Adam,
I would like to know to what extend is the compatibility with bioscope bam files ?
I produce BAM files with the single read pipeline, but Cufflinks still bother me with XS attribute.
It work if i add this specific column with the awk command found in this forum :
Thx for the support you provide in these forums
Thibault
I would like to know to what extend is the compatibility with bioscope bam files ?
I produce BAM files with the single read pipeline, but Cufflinks still bother me with XS attribute.
It work if i add this specific column with the awk command found in this forum :
Code:
awk -F'\t' 'BEGIN { OFS="\t"} {if($2==16) {$(NF+1)="XS:A:-"; print $0,$(NF+1)} else {$(NF+1)="XS:A:+"; print $0,$(NF+1)}}' test.sam > test.sam2
Thibault
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