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When I convert the bam file from the output of tophat 1.1.4 to a sam file, it loses the strand specificity ie,, XS:A+/- at the end. This renders it unusable for cufflinks. The conversion I used is samtools view -h -o out.sam in.bam. Any suggestions?
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The latest version of cufflinks directly accepts the bam file produced by TopHat. you do not need to conver the bam file into sam file. I just did this a couple of days ago.
$./cufflinks -G refGene.gtf accepted_hits.bam
This works quite well -
I am having a similar problem with converted output .sam files. And when I input my .bam directly into cufflinks, I get the following within a second before the process terminates:
Do .bam files have a CIGAR string? Has anyone else encountered this problem?Counting hits in map
CIGAR op has zero length
CIGAR op has zero length
CIGAR op has zero length
Total map density: 0.000000
CIGAR op has zero length
CIGAR op has zero length
CIGAR op has zero lengthComment
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