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Old 12-15-2011, 04:57 AM   #2
arvid
Senior Member
 
Location: Berlin

Join Date: Jul 2011
Posts: 156
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There are two reasons why it doesn't work:

1. "file.unique.bam" is not in the BAM format (look at "samtools view" for correct usage).
2. You stripped the SAM headers with your grep command.

You might need find a better way of filtering for uniquely mapped reads which preserves the SAM headers, or you add the SAM headers back to the header-stripped SAM file you created with your first command afterwards (look at "samtools view").

Then, convert it to BAM with SAMtools and feed it into BEDTools.
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