Hello Everyone,
I made an index and it's respective index stats from a previously sorted BAM File. The BAM file contains the alignment of single-end SOLiD reads to the human genome. What I don't understand is that in the "# of unmapped reads" column of the indexstats output, you can find references with values that differ from 0. (e.g. "gi|251831106|ref|NC_012920.1| 16569 19656 3"). This is weird, becuase I don't understand how a read can be "unmapped" preferentially to a specific reference, instead of being counted as part of the "*" row?
Cheers,
Martin
I made an index and it's respective index stats from a previously sorted BAM File. The BAM file contains the alignment of single-end SOLiD reads to the human genome. What I don't understand is that in the "# of unmapped reads" column of the indexstats output, you can find references with values that differ from 0. (e.g. "gi|251831106|ref|NC_012920.1| 16569 19656 3"). This is weird, becuase I don't understand how a read can be "unmapped" preferentially to a specific reference, instead of being counted as part of the "*" row?
Cheers,
Martin
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