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Dear Dr Fumagalli,
I'm trying to use your plotPCA.R script through:
`Rscript --vanilla --slave pca.R -i ${in}.covMat -c 1-2 -a ${bamclst}.clst -o ${out}.pdf`
with a .covMat file I generated fro…
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I want to begin with thanking you for the very helpful angsd tutorial and scripts, they have been so useful.
I have run your code plotQC.R successfully on my samples but I am struggling with how to…
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Many people study systems with currently no good outgroup sequence available to determine ancestral and derived states of alleles and therefore cannot estimate a derived allele frequency spectrum (SFS…
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This is the same issue as #118, but this has nothing to do with Python3 as in the previous thread.
>**sudo python2 setup.py install**
Traceback (most recent call last):
File "setup.py", line 89…
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Hello,
Trying to compile your software here on an Ubuntu 16.04 box and for some reason the `sem_t` type isn't recognized. It's a standard library so I am not sure what the problem is. My version of…
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Hi there.
Thanks a lot for building up this wonderful package which greatly helped biologist with limited basis for coding like me.
I am trying to run my first test sample, but I met this error:…
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Dear developers,
I am working with ANGSD (version: 0.917-123-gf8b7a92 (htslib: 1.4.1-16-g499245e)), doing some test on the effect of missing data in the inferences. I compute coverage per site of t…
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Hi all,
I am trying to run angsd on my dataset and I keep running into segmentation fault no matter what version I choose to you. So far, I have tried v0.917, 0.918, and 9.920. Please find the comm…
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Hi, i've updated the CPU / chimeric_blacklist.awk script and now get an error on line 223 when running the example.
223: str[j] = and(tmp[2],16);
it may be that and() is not defined in the OS X v…
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Hi!
I'm trying this new function that was added in the latest versions to do PCA only by sampling one single read per site. I was hoping you could clarify this information that is in the wiki:
"Fo…