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relipmoc / skewer

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Not trimming correctly even though perfect match present (example provided) #17

Open andreas-wilm opened 9 years ago

andreas-wilm commented 9 years ago

Hi guys,

I have a read pair with perfect (default) adapter matches that doesn't get trimmed at all no matter which settings I use (see below).

s1.fq: @HS001:1:H27C5BCXX:1:1101:9143:40464 1:N:0:CGGAAT GCCCTGAAAGCGGAGGCGAGCAAAGCCCCCAAGCGTGTCAAACGGCTTTCGATGGTGCTTCTCGTATGCTTTATGCTGATTTATGTGGTGGTGATCGGACAGACACTGCTGTCGTCACTCGGAGGGCTGTTCGGATGAAAGGCTTGAACATGAAAAAATCAGAAAACAAAAGGCAGCCGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGTCTTCTGCTTGAAAAA + AGAGGGGGGIIIGIIGGGGIGIIIIIIIIGIGGGGGGGIIIIGGGIIGIGGGGGGAGGGGIIGGG<GGAGAG.GGIAAGAA.<A.<AGGGAAAGGIAGGGGGAAA.GGGAAGAGA.AGGG.G.A<G.<GGG..AGGGGAGGGGAGGGGGGGGGGGGGGGGGGGIGGAGGGGG.GGAGAAAAGG.GAAGAA.GAGIIGGGGGGGGAGGG.7<GAAGAGAGIIGA.7GGGGIGGGGGGGGG.<GG.<.<A.G

s2.fq: @HS001:1:H27C5BCXX:1:1101:9143:40464 2:N:0:CGGAAT ACCTGCTGCCTTATTTTTTCTGGTTTTTTCATTTTCTTGGCTAACCTGGGAACAGCCCTCCGAGTGGCGCCAGCAGTGTCTGTCCGATCACAACCAGATGATCTCGCATGAAGCATTCTAGATGCACCATCGAAAGCCGTTTGACACGCTTGGGGGCTTTGCTCGCCTCCGCTTTCAGGGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGACGCCGTATCATTAAAAAAAAAA + <AA.G.<.A<.<...<..<AG..GGGA..<....<..............<....<GG.<.<.AAG.........<.<...<<G.<....GA..<<.....<....<G.<..<<A...<.......<..<...<<A.<.<<A<G.<AGGGG<.GAAGG<GAA..<<A<GA.<G.AGGGA.77..7<.<G.AAG...<.77<<A.AA.A..A.<AA.AG.7A7G.G...<<..77AG.7..<AGGG<AAGA

Andreas

PS: cutadapt trims this example correctly

andreas-wilm commented 9 years ago

Correction: -m ap does trim. However, it trims at the wrong site, Also, this is not amplicon data.

Andreas

PS: Could you in addition please clarify somewhere how the 'amplicon' mode works?

relipmoc commented 9 years ago

try to use "-m any", which will trim two paired reads independently