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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
bk11
★
2.3k
Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11"
by
Dylan
•
0
> (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…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Ram
43k
> 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…
Answer: Difference between samtools "-f 9" and "-f 11"
by
Pierre Lindenbaum
161k
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…
Comment: How to convert plink files to Hapmap Format
by
Sofia
•
0
the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser
by
atowns21
•
0
could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
> 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…
Comment: How to convert plink files to Hapmap Format
by
bk11
★
2.3k
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
by
Sofia
•
0
This is how my .fam file looks like ![enter image description here][1]
[1]: /media/images/caccd97c-3606-48d2-aa32-423a9882
And I run …
Comment: How to convert plink files to Hapmap Format
by
bk11
★
2.3k
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…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
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…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
> 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
by
LauferVA
4.2k
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
by
Sofia
•
0
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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