Closed cfriedline closed 5 years ago
The PE adapter list contains the SE adapters, so that doesn't really matter. If people want to add custom adapters, I think I will leave that to editing the code directly. I'm in the process of reworking the documentation and I can add this in there.
Not all of them, though...
$cat TruSeq2-SE.fa
>TruSeq2_SE
AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
>TruSeq2_PE_f
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
>TruSeq2_PE_r
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
$ grep AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG Tru*.fa
TruSeq2-SE.fa:AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
$ grep AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Tru*.fa
TruSeq2-PE.fa:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
TruSeq2-SE.fa:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
TruSeq3-PE-2.fa:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
TruSeq3-SE.fa:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
$ grep AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG Tru*.fa
TruSeq2-PE.fa:AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG
TruSeq2-SE.fa:AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
I think I can finally close this. Version 2.7 and up will use fastp
for adapter trimming and will implement adaptive, auto-detection for adapters. This should fix this issue permanently.
This might be something that isn't easily generalizable across all users, but ran across this today digging through the dDocent wrapper.
ADAPTERS
appear to be set here:Then used here:
Shouldn't this be the SE adapters for SE ddRAD, or at least some choice between which adapter set to use TruSeq2 vs 3, for example? Maybe this is more of a feature request than an issue, but wanted to get it logged. ;-)
This is dDocent
2.24
I'm happy to come up with something, if you want a PR. Just let me know.Thanks!