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Comment: gatk Hardfilter Error
by
Pierre Lindenbaum
154k
the formatting is missing in your question. how do you break lines ? did you add a antislash at the end of the lines ? didn't you forgot th…
Comment: Salmon Index
by
ashleymb1116
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0
Thank you! I've made the decoy before, but I'm trying to redo it since I believe the first time I completed this incorrectly. The page Salm…
Comment: How to make a dotplot for bulk RNA average expression ?
by
LionisOne
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@Trivas Thank you very much for your reply. if you don't mind could you share the script. Because its not showing the dot in my plot. Sorry…
Answer: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Zhenyu Zhang
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800
Where did you get the data from? which reference build and gene model is it using?
There are many versions of TCGA expression data around…
Comment: gatk Hardfilter Error
by
bestone
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A USER ERROR has occurred: Argument output was missing: Argument 'output' is required.
**************************************************…
Answer: How to make a dotplot for bulk RNA average expression ?
by
Trivas
★
1.1k
You'll want to use the `pivot_longer` function in R so that you have three columns: 1) gene, 2) condition, 3) value. You can then use ggplo…
Comment: Salmon Index
by
GenoMax
129k
> can I just use the cDNA file from Ensembl as mentioned above
Yes you can. That said the recommendation from `salmon` devs is to use the …
Comment: Dada2 in Qiime2: losing reads during merging
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andres.firrincieli
3.3k
How long was the amplicon?
If the amplicon is longer than the sum of the two read lengths, the R1 and R2 reads will not merge. By default,…
Comment: Converting RefSeq protein accession IDs into entreZ IDs
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Pegasus
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Thank you @genomax, since efetch function is not supported by the HPC I am working on, I replaced it with the command below;
curl …
Comment: How extract specific SNP position from the bed file-Bedtools
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LionisOne
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@Pierre Lindenbaum Thanks a lot! Its a great help! I will check and let you know.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If
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Joe
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Sounds like you might be better off using something like Mol*:
https://academic.oup.com/nar/article/49/W1/W431/6270780?login=false
https://…
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Alewa
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thank you so much Alex!
Comment: Regular Expression for conversion
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Joe
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Are *all* of your long-form references of *exactly* that format? If not this will be nigh-on impossible.
This is a (non-optimal) regex whi…
Answer: Expected number of haplotype IDs per path in PHG
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lcj34
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FYI: After testing with various parameters we determined the problem was with the backward-forward algorithm of the BestHaplotypePathPlugi…
Comment: How to calculate SARS-2'S evolutionary rate
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Ram
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Your question is as broad as "how to cook Argentinian cuisine in a modular kitchen": no exact details on what you have, what you tried or w…
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