40inner mate distance for paired reads in a bam file

Posted 2020-11-20 renping

参考：https://www.biostars.org/p/106291/#106344

 

1、inner mate distance : the distance from the right most end of the left read to the left most end of the right read

2、the "insert size"=sequence between adapters (actually encompasses R1 and R2 as well as the unknown gap between them) and it is also known that the ninth column of the SAM file (TLEN) represents the insert size

3.1、Insert size = 400

        Library = 2x150bp

        Inner size = 400-2*150 = 100

3.2、So for a 2x100bp library with 193 mean insert, your inner distance is 193-2x100 = -7 (meaning that they overlap by 7bp)

4、

     Insert_size = the sequence betwwn adapters

     Fragment_size= Insert_size + Adapters