Dear All
I mapped my bisulfited DNA sequencing reads by Bsmap, the out put file was SAM format. Before that, I trimmed 18bp repeat reads.But after mapping, some information in the "QNAME" lost.
Here is an example
Trimmed reads mapping
ILLUMINA-XXXXX3:7:FC665XXXXXX:1:1 345 chr17 7111078 255 51M * 0 0 ACACACATACATACACACATACACAGGCCTTCACCAAACACACCCAACGNA BGDGDGGGEGGDDGDGEGGGEHHHHHGGGGGGFGGGGGGGG7<>7>>>(#> NM:i:10 ZS:Z:-+
unTrimmed reads mapping
ILLUMINA-XXXXX3:7:FC665XXXXXX:1:18:11311:15796 153 chr19 42422318 255 101M * 0 0 TGGTGTATGTGGGGTGTACACATACCTCTCATGTATACGCCACATATACACCACACATACCACATATACACACCACAGACAAACCAAACACACCCAACACA DG@BDBBCACFF@FDFFBF3324*53/)'*315/HGEIHDBBDDDBIDI?CC@<EGDECGDBGGDGGBEBG>GG@<BGDFIIEIIIIIIIIHIIIIIIGII NM:i:13 ZS:Z:+-
The red part lost in the sam file which generated by trimmed reads. So someone know what happen here?
Any help would be greatly appreciated!
I mapped my bisulfited DNA sequencing reads by Bsmap, the out put file was SAM format. Before that, I trimmed 18bp repeat reads.But after mapping, some information in the "QNAME" lost.
Here is an example
Trimmed reads mapping
ILLUMINA-XXXXX3:7:FC665XXXXXX:1:1 345 chr17 7111078 255 51M * 0 0 ACACACATACATACACACATACACAGGCCTTCACCAAACACACCCAACGNA BGDGDGGGEGGDDGDGEGGGEHHHHHGGGGGGFGGGGGGGG7<>7>>>(#> NM:i:10 ZS:Z:-+
unTrimmed reads mapping
ILLUMINA-XXXXX3:7:FC665XXXXXX:1:18:11311:15796 153 chr19 42422318 255 101M * 0 0 TGGTGTATGTGGGGTGTACACATACCTCTCATGTATACGCCACATATACACCACACATACCACATATACACACCACAGACAAACCAAACACACCCAACACA DG@BDBBCACFF@FDFFBF3324*53/)'*315/HGEIHDBBDDDBIDI?CC@<EGDECGDBGGDGGBEBG>GG@<BGDFIIEIIIIIIIIHIIIIIIGII NM:i:13 ZS:Z:+-
The red part lost in the sam file which generated by trimmed reads. So someone know what happen here?
Any help would be greatly appreciated!
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