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Old 04-16-2009, 02:12 AM   #3
Layla
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Location: London

Join Date: Sep 2008
Posts: 58
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The file I was referring to was generated using the maq match command. I have re-run the maq match command using the -H and -u options. Do you think the multiple matches should be removed and the maq match command run again or would it be sufficient to remove the multiple matches and move on to do a pileup.

At this stage I shall focus on correctly paired reads (flagged 18), remove multiple hits (flag of 0) and also low mapping quality scores (<30).

Any other suggestions or comments how people would go about cleaning their chip-seq data?

Cheers

L
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