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Recent Replies
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
If you aren't willing to provide more precise information than this, sufficient for a reader to reproduce what you're seeing, I will delete…
Answer: Error while trying to install salmon
by
Chris
▴
10
Donwloading the package from conda (https://anaconda.org/conda-forge/boost/files?version=1.60.0) worked for me
wget https://anaconda.org/…
Answer: finding error to run edgeR, error in ploting MDS and after that in model matrix
by
Gordon Smyth
★
5.4k
First issue is that GEO series matrix files can't be read using `read.delim`.
Second issue is the data are from Agilent microarrays and …
Comment: PLINK2 selecting variants based on INFO score
by
m.c.roozen
•
0
I have tried that (the .pvar file contains the "1:10586" form as ID which I mentioned above) which leads to the same output as above, 0 var…
Answer: samtools markdup in Rsamtools
by
joe
▴
350
You can run any system command from inside R using `system()`. This works well if there is a single command without many dependencies. For …
Comment: samtools markdup in Rsamtools
by
Pierre Lindenbaum
152k
> But other solutions are also fine:
bash, nextflow, snakemake
Answer: samtools markdup in Rsamtools
by
ATpoint
68k
My honest opinion: Do processing of sequencing data on the standard command line with samtools. There is no need for the added complexity t…
Comment: To batch correct or analyse separately?
by
predeus
★
1.8k
Another great and up-to-date resource is this: https://www.sc-best-practices.org/preamble.html
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
The --exclude file must use the same variant IDs as your .pvar file. You should elaborate on what seemed to go wrong when you tried to arr…
Comment: phylogeny
by
炫
•
0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: Issue with hmmcalibrate during tutorial.
by
apcreyes29
•
0
If that's the case then I'll just proceed then. Thank you!
Answer: To batch correct or analyse separately?
by
ATpoint
68k
Instead of writing that all down I recommend to read the relevant part of the Bioconductor scRNA-seq book (OSCA) which covers the "how's" a…
Answer: Issue with hmmcalibrate during tutorial.
by
Mensur Dlakic
★
22k
Pretty sure that `hmmcalibrate` does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual …
Comment: High downstream gene expression
by
yoser4
▴
10
Thank you for your reply.
Your answer has helped me.
I am a novice in scientific research, and the reading of literature is really poor.
…
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