seqkit amplicon flanking has a bug in v2.8.0
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ChristinaGalonska87 commented
Seqkit amplicon is not spitting out the correct flanking region corresponding to a given primer in v2.8.0. Instead it outputs the same sequence, no matter the primer.
shenwei356 commented
Sorry, I can't reproduce this. Could you please give more details, or give some data to test?
$ seqkit seq --rna2dna hairpin.fa \
| seqkit locate -p AAAGCCATCAC
seqID patternName pattern strand start end matched
mmu-mir-679 AAAGCCATCAC AAAGCCATCAC - 35 45 AAAGCCATCAC
ath-MIR854a AAAGCCATCAC AAAGCCATCAC + 162 172 AAAGCCATCAC
ath-MIR854c AAAGCCATCAC AAAGCCATCAC + 162 172 AAAGCCATCAC
vun-MIR160 AAAGCCATCAC AAAGCCATCAC - 60 70 AAAGCCATCAC
rno-mir-679 AAAGCCATCAC AAAGCCATCAC - 62 72 AAAGCCATCAC
$ seqkit seq --rna2dna hairpin.fa \
| seqkit amplicon -F AAAGCCATCAC -r 1:5 -f \
| seqkit fx2tab -i
mmu-mir-679 ACACC
ath-MIR854a GTTTC
ath-MIR854c GTTTC
vun-MIR160 TGTTC
rno-mir-679 ACACC
$ seqkit seq --rna2dna hairpin.fa \
| seqkit amplicon -F AAAGCCATCAC -r -1:5 -f \
| seqkit fx2tab -i
mmu-mir-679 AAAAGCCATCACACACC
ath-MIR854a CAAAGCCATCACGTTTC
ath-MIR854c CAAAGCCATCACGTTTC
vun-MIR160 TAAAGCCATCACTGTTC
rno-mir-679 AAAAGCCATCACACACC
$ seqkit seq --rna2dna hairpin.fa \
| seqkit locate -p AAAAGCCATCACACACC
seqID patternName pattern strand start end matched
mmu-mir-679 AAAAGCCATCACACACC AAAAGCCATCACACACC - 30 46 AAAAGCCATCACACACC
rno-mir-679 AAAAGCCATCACACACC AAAAGCCATCACACACC - 57 73 AAAAGCCATCACACACC