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Comment: Difference between samtools "-f 9" and "-f 11"
by
Dylan
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> (which is weird, if it's in proper pair, read and its mate should be both mapped)
So that was my thought as well, I think the code you l…
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> several single cell samples
At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
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9: read must be paired AND mate must be unmapped
11: read must be paired AND mapped in proper pair AND mate must be unmapped (which is w…
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the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
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@benjamin.pyenson could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you hav…
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> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts.
If you had extraneous sequence…
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bk11
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Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format
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Sofia
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This is how my .fam file looks like ![enter image description here][1]
[1]: /media/images/caccd97c-3606-48d2-aa32-423a9882
And I run …
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What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
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Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
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> linked to a list of grants
Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
Answer: Redirection of Duplicate PMIDs
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LauferVA
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Hi Dominick,
One thing I am not sure of is, how is it that you got the other PMID in the first place?
The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format
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Sofia
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Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
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bk11
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For subsetting a sample, you can do something like this-
Idents(seuratObj) <- "orig.ident"
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Comment: Redirection of Duplicate PMIDs
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LauferVA
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Ok! I have a recommendation. I'll submit it as an answer, pending your feedback.
vincent
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