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Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v
by
fuellen
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20
Hello and Thanks!
OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared".
In any case, is …
Comment: a problem with getBM
by
Mike Smith
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1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`.
It's …
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
•
0
Hello,
I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
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Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
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Fabio Marroni
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2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
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Rob
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
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Pierre Lindenbaum
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> with nucleotide numbers and DNA/prot aligned line by line
what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence
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vvasta
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I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number
w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
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Pierre Lindenbaum
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but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
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Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
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Fabio Marroni
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Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
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Fabio Marroni
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Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
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Pierre Lindenbaum
152k
```
Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
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Pierre Lindenbaum
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I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of
gzip < chr1.vcf.gz > chr1.vcf.gz…
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