weird TLEN

I used bowtie2 to align my paired end sequencing results. However, I am puzzled by the TLEN field as following.

..:1971   99      chr1    10059   2       56M     =       10059   -192  ...

..:1971   147     chr1    10059   2       68S56M  =       10059   192   ...

As the inserted DNA is shorter than read length, both R1 and R2 are mapped to chr1:10059. The TLEN field is 192/-192, but not 56. How is this value calculated?

bowtie2 samtools

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updated 2.9 years ago by GenoMax

• written 2.9 years ago by agreatgoodfellow •

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