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Recent Replies
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
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![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
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Okay, that shows us the problem, but not what we need to solve it.
But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★
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In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1].
[1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴
750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★
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In Plink, A1 is usually a minor allele and A2 a major allele.
.frq (basic allele frequency report)
Produced by --freq.
…
Comment: Raw counts using stringtie
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> Error parsing strand from GFF line
Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data
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I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
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Thank you for sharing.
What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
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> I think I will filter the reads ultimately.
If your data was not run and basecalled using the same exact version of pore/software for a…
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What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
Comment: Do I need to go back and filter my long-reads?
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> I think you should have the right to delete a question you yourself have submitted
If you were to talk to someone, can you make them for…
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I don't have any experience using `BRAKER2` so I cannot comment, but I would be extra careful about data you find on non-model organisms. T…
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You can copy and paste your code and then use `101010` button in the edit window to format it as text to keep it monospaced.
For example …
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ST
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I guess this could really depend on the "counting" strategy, the library complexity and possible lane biases.
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