I’ve been searching the answers in Q2 forum, some clues but still have low confidence that how to fix this issue.
Hiseq 250bp data, paired-end. I think that there are forward and reverse reads in both R1 and R2. I think it would be best is to have the files in the same orientation in each file, but have no idea how to do that by Q2.
Example. Primer VH1_2 (AGGTCCAACTGCAGCAGCC) can be found starting at position 2 in R1 or R2.
One pair where it matches R1.
R1:
@SNL147:722:HGCMVBCXY:2:1106:18591:4974
CAGGTCCAACTGCAGCAGCCTGGGGCTGAGCTTGTGATGCCTGGGGCTTCAGTGAAGCTGTCCTGCAAGGCTTCTGGCTACACCTTCACCAGCTACTGGATGCACTGGGTGAATCAGAGGCCTGGACGAGGCCTTGAGTGGATTGGAAGGATTGATCCTAATAGTGGTGGTACTAA
GTACAATGAGAAGTTCAAGAGCAAGGCCACACTGACTGTAGACAAACCCGCCAGCACAGCCTACATGCAGCTCC
R2:
@SNL147:722:HGCMVBCXY:2:1106:18591:4974
GAGGAAACGGTGACCGTGGTCCCTGTGCCCCAGACATCGAAGTACCAAACCCCGTCCCAGTTTGATCTTGCACAATAATAGACCGCAGAGTCCTCAGATGTCAGGCTGCTGAGCTGCATGTAGGCTGGGCTGGAGGGGTTGTCTACAGTCAGTGTGGCCTTGCTCTTTGACTTCTC
ATTTTACTTAGTACCACCAATATTAGGATCAATCCATCCAATCCACTCAAGGCCTCGCCCAGGCCGCCGCTTCA
One pair where it matches R2:
R1:
@SNL147:722:HGCMVBCXY:2:1106:7141:4616
CAGGTTCAGGTGACCGTGGTCCCTGTGCCCCAGACATCGAAGTACCAGCTCTACTACCGTAGTCCCCTTGCACAATAATAGACCGCAGAGTCCTCAGATGTCAGGCTGCTGAGTTGCATGTAGGCTGTGCTGGAGGATTTGTCTGCAGTCAGTGTGGCCTTGCCCTTGAACTTCCC
ATTGTAGTTAGTATAACTATCAGAAGGATCAATCTCTCCAATCCACTCAAGGCCATGTCAAGGCCTCTGCTTTG
R2:
@SNL147:722:HGCMVBCXY:2:1106:7141:4616
CAGGTCCAACTGCAGCAGCCTGGGGCTGGACTTGTGAAGCCTGGGGCTTCAGTGAAGCTGTCCTGCAAGGCTTCTGGATACACCTTCACTAACTACTGGATAGGTTGGGCAAAGCAGAGGCCTGGACATGGCCTTGAGTGGATTGGAGAGATTGATCCTTCTGATAGTTATACTAA
CTACAATGGGAAGTTCAAGGGCAAGGCCACACTGACTGCAGACAAATCCTCCAGCACAGCCTACATGCAACGCC