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Amazing tool, I really like it since it is fast enough especially when the genome is very large. I am super interested in using this tool to figure out the off targets for Cpf1 and the newly reported …
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Hello,
We're using the RDA function to carry out genome scans for signals of adaptation [similar to this paper](https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13722) - we ar…
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Hello!
I am scanning the human genome for CTCF motifs using a PWM-format matrix:
```console
moods-dna.py --sep ";" -s hg38.fna --p-value 0.0001 -S MA0139.1_pwm -o ctcf_scan
```
File hg38.fna co…
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Hi, thanks for a great package!
I am having some issues when trying to perform runHomer for motif discovery across my clusters.
Here is the code I ran
motifs = runHomer(
CD8.sp[,idy.ls…
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Waiting on more info from Andy.
- Need index integration in all library construction protocols - still thinking that index name might be best for picking but if we could add well location to name tha…
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Looking at realSFS dadi, I notice that it uses the outer product of the 1d SFS as a prior for calling bins/site, rather than accepting a "joint" prior that is >=2 dimensional. I suspect this isn't a g…
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[article](http://www.pnas.org/content/111/18/6744.full): Qin, X.-C. et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. PNAS 111, 6744–6749 (2014…
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Hello!
I am scanning the human genome for the [long CTCF motif](https://jaspar.genereg.net/matrix/MA1929.1/?revcomp=0) (34 bp) using a PWM-format matrix:
```moods-dna.py --sep ";" -s hg38.fna --…
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Hello,
I would like to use BrumiR to identify small RNAs in a species without a reference genome (thanks for developing BrumiR), but get the following error during compilation:
~/brumir$ make al…
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During the run in docker this error occurs:
Traceback (most recent call last):
File "scripts/prokseq.py", line 711, in
main()
File "scripts/prokseq.py", line 600, in main
fn.create…