Bioscope Ma conversion (to base space)

DNAjunk · 04-08-2011, 02:03 PM

Hi

Has anybody written a script/c program that converts mapped color space reads to base space reads by using Bioscope's (vs 1.3.1) mapping file *.ma and the reference fasta file?

I know this could be done also with the maToBam conversion tool, but I am interested in a light/simple script that does the same fast and without using quality files and Bioscope overhead....

Thanks for advice.

westerman · 04-11-2011, 08:21 AM

I am not sure why you would need the reference file for the conversion. The .ma file can be converted from color-space to base-space directly.

I sent you PM with my cs2bs program. Send me email with your real email if the program does not come through properly formated.

DNAjunk · 04-15-2011, 08:29 AM

Thanks, westerman for the script.

I would like to convert the mapped reads into nucleotides and at the same time correcting the invalid color changes by using the reference sequence according to the SOLiD white paper on "Understanding of Two-Base Color Codes..". Similar to the maToGff program (which doesn't work for me) and ma2bam (which works fine but I would like have a simple, light program/script).

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04-08-2011, 02:03 PM	#1
DNAjunk Member Location: Western Europe Join Date: Jun 2009 Posts: 61	Bioscope Ma conversion (to base space) Hi Has anybody written a script/c program that converts mapped color space reads to base space reads by using Bioscope's (vs 1.3.1) mapping file *.ma and the reference fasta file? I know this could be done also with the maToBam conversion tool, but I am interested in a light/simple script that does the same fast and without using quality files and Bioscope overhead.... Thanks for advice.

04-11-2011, 08:21 AM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	I am not sure why you would need the reference file for the conversion. The .ma file can be converted from color-space to base-space directly. I sent you PM with my cs2bs program. Send me email with your real email if the program does not come through properly formated.

04-15-2011, 08:29 AM	#3
DNAjunk Member Location: Western Europe Join Date: Jun 2009 Posts: 61	Thanks, westerman for the script. I would like to convert the mapped reads into nucleotides and at the same time correcting the invalid color changes by using the reference sequence according to the SOLiD white paper on "Understanding of Two-Base Color Codes..". Similar to the maToGff program (which doesn't work for me) and ma2bam (which works fine but I would like have a simple, light program/script).