Questions tagged [shell]
The shell tag has no summary.
168 questions
4
votes
2
answers
59
views
Writing loop to concatenate my reads across lanes
I'm new to bash and trying to check that the way I wrote my code is correct. Any advice is appreciated!
I have a bunch of samples with reads across 2 lanes. I want to be able to just loop through the ...
- 41
1
vote
0
answers
56
views
"java need to be specified" when running CIRIquant
The problem can be solved by simply installing Java, though I still don't understand, why this requirement isn't mentioned anywhere and which role Java plays in this package.
I'm using Ubuntu 22.04.5....
- 11
1
vote
0
answers
34
views
Gromacs to Desmond topology
I need to do analysis for gromacs output MD SIMULATION files by Desmond (so i need out.cms type file)
How to get that from gromacs type files I am trying with intermol and vmd but without benefit any ...
- 11
2
votes
1
answer
127
views
windows shell -- running igblast: "BLAST query/options error: Germline annotation database ... internal_data directory cannot be found"
I'm trying to run igblast from NCBI in windows powershell. When following the documentation and trying to run the following code:
...
- 31
3
votes
1
answer
79
views
Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe
I am trying to use a named pipe to pass data from the Trimmer utility from the AGeNT toolbox from Agilent, through bwa-mem2. The normal behavior is that the Trimmer utility writes trimmed fastq files ...
2
votes
2
answers
98
views
Python/R/bash script to ease the comparison of different protein complexes in PDB
I would like to create a table of comparison among similar protein complexes from the pdb.
This would be based on their numbers of proteins and the presence of each protein.
Is there any way like ...
- 31
1
vote
0
answers
78
views
Need to find an intersect of sequences inside fasta files (no standardized sequence names)
I have several multifasta files (each containing between 3,000 to 3,600 sequences). The sequence names were derived from the genome where the sequence was extracted and they bear no significance or ...
2
votes
2
answers
146
views
How to add corresponding "chr" before location (start, end) of bed alike file?
I have some bed alike files but don't have chr term in the fisrt column, that I want to add chr and its corresponding chromosome ...
- 329
0
votes
1
answer
163
views
How to debug a bash script
Please somebody debug my code
In sub-folders there are 500000 vcf files from which I only need 500 vcf files listed in ...
- 2,242
2
votes
1
answer
86
views
Salmon Multiple File SCRIPT giving error
Hi I am using Salmon quantitation for multiple fastq paired files using following code
...
- 61
1
vote
0
answers
125
views
3
votes
2
answers
448
views
Printing the results of for loop into a txt file
I have a for loop which prints available vcf files in the path for a list of patient IDs (using find dx data function) into my zsh terminal:
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- 2,242
-1
votes
1
answer
63
views
Concatenate multiple fasta files into individual files per unique entry
I have several splitted fasta files like this:
TK273759.fastaaa
TK273759.fastaab
TK273759.fastaac
TK273759.fastaad
TK273759.fastaae
I want to concatenate these ...
-2
votes
3
answers
111
views
Filtering columns from large file based on a column list
I have list of samples as a txt file and want to only keep these samples from this large file; column name is samples name in the large file.
...
- 393
2
votes
0
answers
130
views
Racon: empty overlap set!
Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then ...
- 21