Closed bdelepine closed 6 months ago
Thanks for reporting this. It's a bug introduced in v2.8.0, that occurred when more than 2 pairs of primers were given. Fixed now.
$ seqkit amplicon -p arr.txt seq.fasta --bed
[INFO] 2 primer pair loaded
seq1 0 18 arr1 0 + ATGCGCTATATATATTTT
seq2 0 18 arr2 0 + GGGGAGTGTGTGTGTTTT
Hi @shenwei356,
I have noticed the same issue, even with the latest download of SeqKit.
After downloading the seqkit_linux_amd64.tar.gz link you have above, I tried to replicate the issue and it still does not seem to be working correctly.
With the two primer pairs in a file, there is no output:
cat seq.fasta | seqkit amplicon -p arr.txt --bed
[INFO] 2 primer pair loaded
seqkit amplicon -p arr.txt seq.fasta --bed
[INFO] 2 primer pair loaded
However, both for the command line input and the file input for one primer pair, it works as intended:
File with one primer pair:
arr1 ATGC AAAA
seqkit amplicon -p arr.txt seq.fasta --bed
[INFO] 1 primer pair loaded
seq1 0 18 arr1 0 + ATGCGCTATATATATTTT
The commands used for one primer pair:
seqkit amplicon -F "ATGC" -R "AAAA" seq.fasta --bed
[INFO] 1 primer pair loaded
seq1 0 18 . 0 + ATGCGCTATATATATTTT
seqkit amplicon -F "GGGG" -R "AAAA" seq.fasta --bed
[INFO] 1 primer pair loaded
seq2 0 18 . 0 + GGGGAGTGTGTGTGTTTT
Gosh, seem like I uploaded the wrong binaries. Sorry for this!
No worries, thanks!
Hi everyone,
I encounter an unexpected behavior of
seqkit amplicon
:seqkit amplicon -p
returns a different result thanseqkit amplicon -F -R
.seq.fasta
These commands produce the expected output:
However, if we introduce a file to store the primers, we do not get the same results: arr.txt
It looks like the sequence seq2 is misreported as a valid amplicon of arrangement arr1; whereas I would expect seq1 to be reported, as in the -F -R example. Tested on 2.7.0. The same behavior may be observed without the --bed option.
Am I missing something?
HTH