Hi all,
I have done alignment using Maq and have generated .map files, now I want used the aligned read to generate peaks using MACS.
For doing this I thought of converting .map file to .sam files using maq2sam command, but it showing error as unrecognized command. I have samtools installed in my system and have used samtools previously also but for maq2sam its not working, what wrong am I doing ???
Is there any other method to convert .map files to convert either .sam or .bed so that I can use them in MACS
I have done alignment using Maq and have generated .map files, now I want used the aligned read to generate peaks using MACS.
For doing this I thought of converting .map file to .sam files using maq2sam command, but it showing error as unrecognized command. I have samtools installed in my system and have used samtools previously also but for maq2sam its not working, what wrong am I doing ???
Is there any other method to convert .map files to convert either .sam or .bed so that I can use them in MACS
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