Hello! I discovered a bug when using primer sequence with small caps which was not reverse complementing properly. This was causing cutadapt to truncate some random 10 base pairs from my reads. I hadn't discovered this bug until I saw the cutadapt log and presumably people would rarely use small caps so they wouldn't encounter this.
You can see that the tr command's regex (1st arg) and substitutions (2nd arg) are not of the same length. This us because of a few missing letters..
ATUGCYRSWKMBDHNatugcyrswkbdhvnTAACGRYSWMKVHDBNtaacgryswmkvhdbn
This needs to be fixed by changing the tr's first argument (regex) from
ATUGCYRSWKMBDHNatugcyrswkbdhvn to
ATUGCYRSWKMBDHVNatugcyrswkmbdhvn in multiple occurrences of lines FWD_RC= and RVS_RC= in both cutadaptsmk files.
In summary, this is the modified tr code
tr '[ATUGCYRSWKMBDHVNatugcyrswkmbdhvn]' '[TAACGRYSWMKVHDBNtaacgryswmkvhdbn]' |rev
Hello! I discovered a bug when using primer sequence with small caps which was not reverse complementing properly. This was causing cutadapt to truncate some random 10 base pairs from my reads. I hadn't discovered this bug until I saw the cutadapt log and presumably people would rarely use small caps so they wouldn't encounter this.
The issue is in these lines
You can see that the
tr
command's regex (1st arg) and substitutions (2nd arg) are not of the same length. This us because of a few missing letters..ATUGCYRSWKMBDHNatugcyrswkbdhvn
TAACGRYSWMKVHDBNtaacgryswmkvhdbn
This needs to be fixed by changing the tr's first argument (regex) from
ATUGCYRSWKMBDHNatugcyrswkbdhvn
toATUGCYRSWKMBDHVNatugcyrswkmbdhvn
in multiple occurrences of linesFWD_RC=
andRVS_RC=
in bothcutadapt
smk
files.In summary, this is the modified tr code
tr '[ATUGCYRSWKMBDHVNatugcyrswkmbdhvn]' '[TAACGRYSWMKVHDBNtaacgryswmkvhdbn]' |rev