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Recent Replies
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
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GenoMax
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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
by
dsull
★
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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
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?
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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.
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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.
If e.g., EM is used to guide…
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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…
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dsull
★
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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…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
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![The below image contains the code and result also.][1]
[1]: /media/images/96562b96-d508-4f67-96d1-7c71aa17
Comment: High Malat-1 expression in single cell data
by
dsull
★
6.0k
My response above was actually partly inspired off of a reading of your paper :)
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