Hi,
if you use the "-o" option of htseq-count you generate a sam file that contains an extra column "XF" that contains the feature for each read alignment. Maybe that is what you are looking for?
You can simply create a tab delimited file using "cut -f1,15 <SAM>" from this file telling you which read corresponds to which feature.
Ben
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Tools that report read count AND read names that map to genomic features.
htseq-count and coverageBed are excellent tools for reporting just how many reads map to each genomic features.
How ever to my knowledge the could not report the read names that correspond to the count. Is there any tools that does that?
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