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
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