I ran gmapper-ls from shrimp 2.0.2, and got this SAM output
How can one QNAME have two different query sequences? Is this because of clipped alignment?
The original (fastaq, now supported by SHRIMP) is
This is the same as the second of the two alignments above, but where did the first come from?
Code:
HTS2_0006:2:1:985:6502#0/1 16 chr4 97954288 255 11S24M1S * 0 0 NNNNNNTNNGNCATTTGTAGTTTTCTTTGAATGCTN #################################### AS:i:140 H0:i:1 H1:i:2 H2:i:0 NM:i:4 NH:i:11 IH:i:10 HTS2_0006:2:1:985:6502#0/1 0 chr4 30318022 255 2S21M13S * 0 0 NAGCATTCAAAGAAAACTACAAATGNCNNANNNNNN #################################### AS:i:135 H0:i:1 H1:i:2 H2:i:0 NM:i:3 NH:i:11 IH:i:10
The original (fastaq, now supported by SHRIMP) is
Code:
@HTS2_0006:2:1:985:6502#0/1 NAGCATTCAAAGAAAACTACAAATGNCNNANNNNNN + ####################################
Comment