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Old 11-10-2010, 07:33 PM   #2
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
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bam to sam conversion is easy with samtools

Code:
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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