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Functions that produce very large counts, especially those that _estimate_ very large counts, should return these not as an `igraph_integer_t`, but as an `igraph_real_t`. This ensured that we don't ov…
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_Note:_ This idea originated from the bottom of https://github.com/CAST-genomics/haptools/issues/73#issuecomment-1521143097
Once PGEN files can store multiallelic dosages, we should consider crea…
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### Setup
Biopython 1.7.0, Python 2.7.13, and Mac OSX 10.12.6
I am trying to run the MEME parser on a file with protein motifs, but it returns a KeyError with 'X'.
The protein motifs occasional…
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For some datasets, oligo-analysis returns highly significant k-mers, but
- the assembled matrix is of poor complexity (basically, the matrix contains a succession of Gs)
- `position-analysis` retur…
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Hi,
I ran the ```dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2``` modified model from Dorado. And I use modkit to generate the bed file including 4mC and 5mC positions using this command:
```
mod…
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Dear author,
I have downloaded motif files from JASPAR database and the format is like:
```
>MA0002.3 Runx1
A [ 123 57 0 87 0 17 10 131 500 ]
C [ 1072 …
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`teloclip-extract` will write reads with terminal clipped-overhangs to fasta files. To aide in sanity checks we should include some metadata to the fasta header.
Proposed fields:
- Anchor len: how…
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Hello, when I was running the example of 10X_brain_5k in the step of `runChromVAR()`, an error occurred:
> x.sp@mmat = runChromVAR(
+ obj=x.sp,
+ input.mat="pmat",
+ genome=BSgenome.Mmusculu…
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A shifted count label may be helpful for visualizing the TR sequence and the flanking sequences.
Users can add flanking regions as input motifs, and the count label can be shifted by 1 and ended 1 …
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Running TRGT v0.8 on a custom catalog that includes loci with several adjacent motifs, I found this row in the output vcf throws off my parsing script:
```
chr1 119049087 . AAAAAATAAAATAAAATAAAAT…