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Bealign has a "-R" flag which also aligns the reverse complement of each query sequence, returning it if the alignment is superior. Can you add that to cawlign too? Thanks.
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When supplying a reverse complemented sequence, typeloader complains about a missing UTR. Would be nice if it could say that the sequence seems reverse complemented (if not outright reverse complement…
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Hi,
thanks for the very useful tool, pafCoordsDotPlotly.R. Would it be possible to colour reverse complement and forward alignments differently, e.g. red/blue. I can change the R code myself if you…
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I analyzed the intact seq extracted by LTR_retriever with the command 'TEsorter acau.intact.fa -db rexdb-plant -p 36 -rule 70-30-80'. After splitting the sequence into 72 pieces and translating it, an…
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It isn't clear how hierarchical designs are handled in terms of strand directionality. So if there is an engineered region in the top level that then has its orientation flipped to the lower strand, w…
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@ahwagner raised in the VRS/VCF meeting the idea of reverse complementing sequences and making them available in refget. The idea being if you are going to refer to an event on the opposing strand, su…
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Hello,
Thank vcf2fasta for doing a great job! However, when I tried to extract individual UGGT2 CDS based on vcfs, I found that the start codons extracted were not ATG. The same situation also occ…
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Nice, but does not seem to attempt to RC the barcode sequence during matching. Would be great to have that done automatically
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Hello!
I'm working with a portion of the COI gene in ants, and have been using minibar to demultiplex my reads. We've developed our own indexes, here's an example of what they look like from my inp…
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Hi, I am using Cutadapt 4.9 version installed in an conda environment. I have some follow questions and I am getting confused on how to trim the adapters. I have adapter information from the paired en…