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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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:
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 length
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