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1 vote

Retrieving NCBI Taxa IDs from refseq or GenBank assembly accession

Bumped into this question and tried @michael-hall 's answer, which works, but takes a very long time to execute if you only do one accession number per query, and there is a limit to how many you can ...
Michael D. M. Dryden's user avatar
1 vote

Fixation index calculation from the vcf files

Reviewing the source code, I observe the following at and before line 45 where your error occurs: ...
Maximilian Press's user avatar
0 votes

Visualise multiple disappearing pdb files in Pymol

try: ...
pippo1980's user avatar
  • 1,108
1 vote

Python/R/bash script to ease the comparison of different protein complexes in PDB

OK using PDBx Python Parser and .cif of 1ffk , 1w2b , 3cxc and 1ffM.cif that is modded 1fkk where first row reads: ...
pippo1980's user avatar
  • 1,108
1 vote

Python/R/bash script to ease the comparison of different protein complexes in PDB

for complexes like 1FFK , .cif file : 1FFK.cif think you can try to parse each PDBx/mmcif file and extract what you need from this loop_ of the file : ...
pippo1980's user avatar
  • 1,108
3 votes

Running multiple sequence using spades.py on an HPC

The job array is a formal approach to solving this via SLURM What I am not clear about is the number of files SRR8599992_1.fastq.gz ...
M__'s user avatar
  • 12.6k
1 vote

Multi-pattern search in aligned sequences

Maybe a job for seqkit locate. Here -m 0means no mismatches allowed. I do not understand really your output format, so maybe ...
ATpoint's user avatar
  • 1,430
1 vote

Multi-pattern search in aligned sequences

I wonder if FIMO might be something that you could use. The online version doesn't have the capacity 70 deal with 700GB of data, but you could try it out with a subsample to see if the output is ...
Laura's user avatar
  • 937
5 votes

Running multiple sequence using spades.py on an HPC

I have some time now, so I'm going to take a shot at this, @M__ You need to run spades per read pair. When you specify *_1.fastq.gz as the ...
Ram RS's user avatar
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