5
votes
How to loop over certain files within a directory that belongs to certain samples
You can certainly use a for loop for this if desired, but an easier method is to use the cat command - something like this:
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- 782
4
votes
How to debug a bash script
The first two digits of vcf file names defines which sub-folder they are located.
You could use this information to edit temp.txt so it contains the full path:
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- 497
2
votes
How to parse hmmsearch output?
The TSV output should be sorted by default in a way that for a given query the top hit comes first, followed by other hits. For a quick extraction of top hits you may use a rather simplistic script:
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- 328
1
vote
How to parse hmmsearch output?
Since we don't know what you are trying to maximize here, which of the various columns would define the "best" hit for what you are trying to do, here is a generic solution that will just ...
- 10.1k
1
vote
Increasing memory usage in AWS instance
You need to diagnose for low memory and consider switching to an R5 processor that prioritises memory. Basically it's easily solvable by switching hardware. There are certainly alot of other ...
M__♦
- 12.3k
1
vote
1
vote
Accepted
How to use Gblocks for trimming single-copy gene sequences?
Basically this is 16S data. If its proteins there's a different strategy - even if the data set needed is nucleotides (separate question). I would simply use trimal which is available on conda
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M__♦
- 12.3k
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