Hi,
I have sequenced many RNA paired-end reads, and mapped to genome reference sequence, and now I want to know whether the read is mapped correctly. And from the read identifier, for example: chr1:
4847775
-4887990W:NM_001159750:
1
:
2668
:
917
:
1137
:S/
2, I know this read is come from the range [4847775,4887990],and the segment range is [917,1137], but I am still not clear how to get the exact genomic start position of the read? Is it possible to get it from the read identifier? If not, is there a way to get the exact genomic start position of a read? Thank you very much.
1 Comment
Micha Sammeth
Dear Chong,
the genomic positions of the origins for all sequenced reads are in the BED file which is output after sequencing.
See http://sammeth.net/confluence/display/SIM/.BED+Mapping+Locations