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Old 01-20-2011, 07:42 AM   #1
calexand
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Location: UK

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Default MAQ .map files to .bed/.sam for MACS

Hello,

I would like to use the output .map of a MAQ alignment of unpaired reads as input for the MACS peak caller, and so I want to convert the .map files (binary or txt) to any format recognized by MACS:

"BED" or "ELAND" or "ELANDMULTI" or "ELANDMULTIPET" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE"

If you know a tool for it I would appreciate an advice .

Thank you!
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Old 01-20-2011, 08:14 AM   #2
calexand
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Default

I found this command used after mapview, from a tutorial written by Mali Salmon-Divon and Christiana Spyro.
Weird to answer to myself but perhaps somebody else might find it useful.

awk '{print $2 "\t" ($3-1) "\t" ($3+25) "\t" "*" "\t" "*" "\t" $4}' filet.map > file.bed
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