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I need to annotate some indels for chromosome 22, and then scale this step to the full human genome. I'm running vep locally using snakemake in a HPC environment with 75Gb of RAM. The input file has ~…
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I make a test data. list :
The gff3 file(test.gff) :
Fvb1 GeneMark.hmm3.161109 gene 1 1906 . + . ID=gene31665;Name=gene31665
Fvb1 GeneMark.hmm3.161109 mR…
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Issue reported by email from [Scott Brown](http://www.holtlab.ca/personnel.html#scottb):
>I have a question regarding the protein sequence output from Isovar. I have seen multiple cases where th…
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Hi. I got the following errors in the quantification step.
> IRFinder-1.2.5/bin/IRFinder: line 562: 49201 Broken pipe gzip -cd "$1"
49202 Aborted (core dumped) | "…
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The rowRanges of the SingleCellExperiment output by scUTRquant seems to not capture the 3'UTRs of the transcripts. For example, the 3'UTR length of the ENST00000621592.8 transcript is 1993 according t…
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I have several sequences of codons that I want to remove, not necessarily a pattern within the whole sequence. The codon sequences are all 3 long (9 NT). I am having trouble finding a solution. I ofte…
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I'm puzzled and need help understanding. Consider [NM_015068.3](https://www.ncbi.nlm.nih.gov/nuccore/NM_015068.3). I think that the exons given in the CDOT JSON skip one base that needs to be in the C…
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# **OrthoFinder version 2.5.4 installed by conda:**
```
$ orthofinder -f rep_type_out_more_genomes_faa -M msa -S mmseqs -a 10 -o rep_type_out_more_genomes_faa_orthofinder_test
OrthoFinder versi…
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Hello, I'm trying to calculate CU for ribosomal genes, but it only shows "self".
`milc
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The code that should be modified is shown in the figure
