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Old 05-14-2011, 09:19 AM   #1
Mamoon Rashid
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Location: KSA

Join Date: Feb 2011
Posts: 8
Unhappy Problem mapping to multifasta reference file

Hi,
I mapped short reads (105*2) with BWA to reference genome having two chromosomes in the same file. Everything is fine, except when i load the BAM and VCF file to reference multifasta in Artemis, I rarely see any reads mapped on Chromosome 2.
Then, I mapped reads on single chromosome 2 containing file and (as i expected) i can see lots of reads mapping to chromosome2.
Could any of you point out why i cant see reads mapped to Chromosome 2 when i mapped reads to single file containing both chromoseomes??
I checked @SQ lines in SAM file, these are there.
Thanks
Mamoon
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