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Old 10-19-2010, 10:36 AM   #1
ilyagoldin
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Default SHRIMP 2 SAM output

I ran gmapper-ls from shrimp 2.0.2, and got this SAM output

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
How can one QNAME have two different query sequences? Is this because of clipped alignment?

The original (fastaq, now supported by SHRIMP) is

Code:
@HTS2_0006:2:1:985:6502#0/1
NAGCATTCAAAGAAAACTACAAATGNCNNANNNNNN
+
####################################
This is the same as the second of the two alignments above, but where did the first come from?
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Old 10-20-2010, 05:07 AM   #2
kmcarr
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Default

The first alignment is to the reverse strand of your reference so it is showing the reverse complement of your query sequence.
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