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Old 08-19-2009, 12:22 PM   #1
baohua100
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Default MAQ's mapview format to binary map format

maq map aln.map ref.bfa reads.bfq

maq mapview aln.map > aln.out

The aln.out is text file and aln.map is binary file.

I filter some reads in aln.out and want to convert the new aln.out to .map file.

Because pileup command need .map file.

How can I convert .out to .map ?
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Old 08-19-2009, 01:25 PM   #2
jnfass
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I know of no way outside of a custom script, and I don't know who's written one.

Alternatively, you could just pool the reads that you want to leave in the set, and redo the map command with only those reads.
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Old 08-19-2009, 01:25 PM   #3
nilshomer
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Quote:
Originally Posted by baohua100 View Post
maq map aln.map ref.bfa reads.bfq

maq mapview aln.map > aln.out

The aln.out is text file and aln.map is binary file.

I filter some reads in aln.out and want to convert the new aln.out to .map file.

Because pileup command need .map file.

How can I convert .out to .map ?
Why not convert the .map to .sam, then filter, then to .bam. Using the SAM format is probably better supported.
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Old 08-06-2010, 01:12 AM   #4
UltimaSeq
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Default Convert .mapview to .map

Hi everybody!
I've seen the post is not so current but I hope someone could help me and answer

I've got the same above problem..that is to have done the alignment by MAQ obtaining the .map file and then converted it in the .mapview file in plain text...

Now I've filtered some reads acting on the mapview file and i need the .map to call consensus and snp calling by MAQ...

Coz the conversion to the .sam needed a lot of time (expecially for my files of 35GB each!! ) and i don't trust so much these kind of "masked" conversion..there is nobody who know how to re-obtain the .map binary file of MAQ without redo the alignment (too slowly!!)??

Thanks a lot!
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