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Recent Replies
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
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
★
2.4k
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
★
2.4k
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
by
GenoMax
142k
> 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
by
dsull
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6.0k
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
by
carolofharvest
▴
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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…
Comment: Do I need to go back and filter my long-reads?
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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…
Comment: Raw counts using stringtie
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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?
by
Ram
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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…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★
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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…
Comment: Differential Expression Analysis using DESeq2 in R
by
GenoMax
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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 …
Comment: Same sequencing sample in multiple lanes. How to analyse it?
by
ST
•
0
I guess this could really depend on the "counting" strategy, the library complexity and possible lane biases.
If e.g., EM is used to guide…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
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Hi dthorbur, thanks for the response. I have run Augustus using Arabidopsis as a species. I would like to know about the suitability of usi…
Comment: How does gene length effect the number of reads mapped
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Alicia Oshlack has done some cool work on this but even the plots in her papers show that TPMs sometimes overcorrect and the relationship i…
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