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Hi Hyphy team,
I installed hyphy 2.5.1 and was trying to run BUSTED as described in the current release tutorial. Instead of running a full tree analysis, I wanted to test a subset of branches. I n…
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Hello !!!
I started using riboWaltz a week ago!!! Thanks a lot for such a nice tool!!
I am having a problem when introducing the fasta file for functions like _codon_usage_psite_ as I am getting…
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When hal2maf is used with the --maxRefGap option, in blocks in which the reference species has only gaps the aligned sequences in the other species are on the wrong strand, i.e., the opposite strand f…
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Hi
I just started working on riboseq data, and came across ribo-tish which seems really useful for QC-ing. I have aligned my reads using STAR as per the guidelines and using the gtf annotation file…
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Stumbled into a pretty weird behaviour. I re-run CAT on a previously successful data set. With commit d6af6d0abf4fd3ce9450f51355e18eaeee0ce00e now I only get protein_coding or unknown_likely_coding. T…
fbemm updated
4 years ago
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Hello,
Could you please help me with this:
I want to align the core sequences from each bacterial strain that I used in my study and plot a phylogenetic tree based on alignment of sequences. How…
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bcftools csq (1.10.2) fails with "Error: CDS overlap in the transcript 0: 266-13468 and 266-13483"
for below GFF file. Does this mean that overlapping transcripts are not suported? Could this easily …
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If we define whole/complete/full sequences as those spanning the first base of the (germline) V gene until the last base of the (germline) J gene [as per https://github.com/airr-community/airr-standar…
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I specified a partition file (all.aln.part5.partition) of five partitions in RAxML-style format:
GTR+G, 1stpos = 7910-8590\3, 7749-7952\3, 5319-6863\3, 6997-7680\3, 8590-9373\3, 14120-15259\3, 2769-3…
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The TAP1 and TAP2 protein alignments identify the N-terminal Methionine as position 0, but in the respective nucleotide alignments, the corresponding sequence is correctly identified as codon 1.
I…