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Old 11-10-2010, 07:33 PM   #1
Location: lasvegas

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Default the tophat generate the bam file instead of sam files?

I have a question:

when i trying to use tophat (to alignment in order to generate the SAM file when can be loaded into the cufflinks.Why the output only gives me bam files in the default sub-directories? Is there any way to generate the SAM file? or i have used the wrong parameters? I am using tophat 1.1.0

dingkai0564 is offline   Reply With Quote
Old 11-10-2010, 08:33 PM   #2
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bam to sam conversion is easy with samtools

samtools view -h myfile.bam > myfile.sam
In any case, the current version of cufflinks will accept BAM, but the online documentation doesn't seem to reflect that yet. But I just successfully ran a bunch with bam as input (successfully=cufflinks ran; I haven't looked at the output yet).
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