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.


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  1. 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