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Comment: bedtools intersect by position & stand not working even with common regions
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are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files
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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…
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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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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)'.
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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…
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Using `bedops --intersect` and `gtf2bed` will get their common genomic space:
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```bash
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> System Information: Ubuntu 22.04 (WSL2)
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Did it affect the bamtofastq output file? if so how did you solve the problem?
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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
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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…
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Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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