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When I zip the Homo_sapiens.GRCh38.dna.primary_assembly.fa to .gz file and add this link in the download.sh, it will show the error: gzip: stdin: not in gzip format.
If I use .fa file directly, …
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After last two commits in recent days, I'm not able to successfully run `prepare_annotation_files` method (each of the updates introduced another error):
common initialization:
```
# to have all …
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Hi,
I am using angsd to produce fasta sequences, these are automatically gzipped fasta files.
If I open the fasta file with R-Biostrings the sequence compositon looks like this:
```
dna alph…
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In our experiment, we cross-linked chromosome fragments that may interact in three-dimensional space, basecalling with dorado and identifying methylation information. I need to split the cross-linked …
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```
As discussed on the forum:
https://groups.google.com/forum/#!topic/ruffus_discuss/ErfMSsKNFB4, this
parameter would specify a folder to put all intermediate/final files. Currently
it can be don…
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Hello!
Thank you for this brilliant tool.
I've been using it for an application in which syntenies inferred using `mummer`'s `nucmer` (so, at the DNA-level) were partial, when compared with `mumme…
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- [ ] Datasets
- [ ] AlphaFold 3 PDB dataset
- [x] PDB mmCIF filtering script (`scripts/filter_pdb_mmcifs.py`)
- [x] Fix periodic residue count-chemical component coun…
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```
The ccpn chem_comp xml files exist for residue 63h and 63g, but Format
Converter isn't reading them. I get the following message in the log file. Is
there a setting to check for the path for a n…
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I am getting the following error when running: `prefetch SRR2078863 -O temp`
```
2024-11-07T18:52:46 prefetch.3.1.0: Current preference is set to retrieve SRA Normalized Format files with full b…
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Hi,
I used conda version of 3D-DNA (version 190716) to scaffold my genome.
However, I have not got FINAL files including FINAL.fasta, FINAL.hic although no errors were not observed in log file.
…