Hi,
I masked a sequence using repeatmasker, where it replace regions with 'N' which it wanted to masked. After that I used bwa to map reads back to sequence. SAMTOOL displayed some region of sam file as following:
SRR329951.3160235 16 * 1 37 99M * 0 0 ATGATCTACCCATTGTTACATGAGTGTGGTTTCAACACTACTCTGTATATAGAGACACATTTATGTCCACATCTTAAACGTCTAGTCCTTCTAGGTGTT CCC##########CCC3CCCCCCACC?CAB@:AB?CCCCBCCDCCCBCCDACC=CCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i
In the second column it idicates that sequence being reverse complemented and third column indicates that it is mapping to "*" or undefined region.
can anybody suggest what this could mean or if you have experienced the same then tell me the reason why this could have occur?
I masked a sequence using repeatmasker, where it replace regions with 'N' which it wanted to masked. After that I used bwa to map reads back to sequence. SAMTOOL displayed some region of sam file as following:
SRR329951.3160235 16 * 1 37 99M * 0 0 ATGATCTACCCATTGTTACATGAGTGTGGTTTCAACACTACTCTGTATATAGAGACACATTTATGTCCACATCTTAAACGTCTAGTCCTTCTAGGTGTT CCC##########CCC3CCCCCCACC?CAB@:AB?CCCCBCCDCCCBCCDACC=CCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i
In the second column it idicates that sequence being reverse complemented and third column indicates that it is mapping to "*" or undefined region.
can anybody suggest what this could mean or if you have experienced the same then tell me the reason why this could have occur?
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