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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
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Mark
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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…
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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.
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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...
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GenoMax
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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
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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
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Tully
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```bash
# Obtain the makefile
curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile
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make vcf
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Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
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> 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
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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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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)
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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)
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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
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Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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