Hi all,
I'm using bwa for mapping SOLiD paired reads to the reference genome. After going through the bwa aln and bwa samse/sampe stages I get output in the SAM format. Is this SAM output in colorspace? If so are there tools to convert the SAM format to nucleotide space so that I can generate pile ups in nucleotide space?
Eg. of the output I'm getting for a mapped single-end read is as follows:
./fastq_files/Part_0:6_32_1000 0 chr6 112832228 37 49M = 112832228 0 TNTAGGTAGTGTATTAAATGGCGACAGGACTGGGGGACCCCAGCGCCAA @!9:79,676=*+98:&2(>;5&315+(9:41+8>58-5<18745;0)+ XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:1T35A5T5
Here columns 10, 11 which report the query sequence and the qualities are shown in color space
Any help would be appreciated.
Thanks
N
I'm using bwa for mapping SOLiD paired reads to the reference genome. After going through the bwa aln and bwa samse/sampe stages I get output in the SAM format. Is this SAM output in colorspace? If so are there tools to convert the SAM format to nucleotide space so that I can generate pile ups in nucleotide space?
Eg. of the output I'm getting for a mapped single-end read is as follows:
./fastq_files/Part_0:6_32_1000 0 chr6 112832228 37 49M = 112832228 0 TNTAGGTAGTGTATTAAATGGCGACAGGACTGGGGGACCCCAGCGCCAA @!9:79,676=*+98:&2(>;5&315+(9:41+8>58-5<18745;0)+ XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:1T35A5T5
Here columns 10, 11 which report the query sequence and the qualities are shown in color space
Any help would be appreciated.
Thanks
N
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