Closed hoelzer closed 2 years ago
yep just add the line:
https://github.com/replikation/poreCov/blob/master/workflows/process/seqrs.nf
nothing fancy :D
Hah okay, easy thx for the hint ;)
Ah just wonder if there is an issue w/ your script because the input bed are a bit different:
(base) ➜ poreCov git:(V4_primers_out) ✗ head data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.bed
MN908947.3 30 54 nCoV-2019_1_LEFT nCoV-2019_1 +
MN908947.3 385 410 nCoV-2019_1_RIGHT nCoV-2019_1 -
MN908947.3 320 342 nCoV-2019_2_LEFT nCoV-2019_2 +
MN908947.3 704 726 nCoV-2019_2_RIGHT nCoV-2019_2 -
MN908947.3 642 664 nCoV-2019_3_LEFT nCoV-2019_1 +
MN908947.3 1004 1028 nCoV-2019_3_RIGHT nCoV-2019_1 -
MN908947.3 943 965 nCoV-2019_4_LEFT nCoV-2019_2 +
MN908947.3 1312 1337 nCoV-2019_4_RIGHT nCoV-2019_2 -
MN908947.3 1242 1264 nCoV-2019_5_LEFT nCoV-2019_1 +
MN908947.3 1623 1651 nCoV-2019_5_RIGHT nCoV-2019_1 -
(base) ➜ poreCov git:(V4_primers_out) ✗ head data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.primer.bed
MN908947.3 25 50 SARS-CoV-2_1_LEFT 1 + AACAAACCAACCAACTTTCGATCTC
MN908947.3 408 431 SARS-CoV-2_1_RIGHT 1 - CTTCTACTAAGCCACAAGTGCCA
MN908947.3 324 344 SARS-CoV-2_2_LEFT 2 + TTTACAGGTTCGCGACGTGC
MN908947.3 705 727 SARS-CoV-2_2_RIGHT 2 - ATAAGGATCAGTGCCAAGCTCG
MN908947.3 644 666 SARS-CoV-2_3_LEFT 1 + GTAATAAAGGAGCTGGTGGCCA
MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT 1 - GCCAATTTAATTTCAAAAGGTGTCTGC
MN908947.3 944 966 SARS-CoV-2_4_LEFT 2 + GTGTATACTGCTGCCGTGAACA
MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT 2 - ACAACAGCATTTTGGGGTAAGTAAC
MN908947.3 1245 1266 SARS-CoV-2_5_LEFT 1 + TGAAACTTCATGGCAGACGGG
MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT 1 - TTGATGTTGACTTTCTCTTTTTGGAGT
but this we can also test
as long as it is a correct bed file, it shouldn't be an issue. I use biorust to gather the bed file information. so i don't really parse anything out of it by e.g. columns or so.
we can discuss this further here: https://github.com/replikation/seqrs (code: https://github.com/replikation/seqrs/blob/main/src/main.rs)
seems to work fine, see #153 I do some more test and then merge
I just noticed that, should be relatively easy to also provide potential "repair primers" for V4?