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DNAjunk

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Join Date: Jun 2009

Posts: 62
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#1

bioscope ma to bam conversion

01-12-2011, 08:01 AM

Hello

I have got a question related to the ma2bam conversion.

Is it somehow possible the output the raw read sequence and its quality values in the bam file (i.e. 50 bases) and not only the bases that were aligned to the reference during the mapping? Is there a parameter like ma.to.bam.XXX = ???

In my bam file there are many reads of length 48 bases for example, although the raw read length is 50.

Many thanks for help and kind regards!
Tags: bam, bioscope, length, raw, read
DNAjunk

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Join Date: Jun 2009

Posts: 62
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#2

01-14-2011, 01:27 AM

solved: the full length color-space-coded reads are present in the bam file with the attribute CS:Z:
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