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Comment: bedtools intersect by position & stand not working even with common regions
by
rfran010
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830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files
by
rfran010
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830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly.
If it's not done alre…
Answer: vcf.gz to vcf
by
Mark
★
1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names?
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Jiyao Wang
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You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow?
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Mark
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Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'.
Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
GenoMax
134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
Alex Reynolds
35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space:
```
bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
```bash
# Obtain the makefile
curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile
# Run the makefile
make vcf
```
Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
> System Information: Ubuntu 22.04 (WSL2)
>
> Shell: zsh
>
> Installation Verification: Yes, doctor.py OK
[1]: https://www.biostarhand…
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Reem
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Did it affect the bamtofastq output file? if so how did you solve the problem?
Thanks
Answer: How to import bigwig files into igvR
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Trivas
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You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
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by
Jeremy Leipzig
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0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
•
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Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
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Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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