Use this tag for questions relating to common bioinformatics tasks performed on a *nix system. Things like manipulating/converting between standard biological text formats, extracting data of interest from such formats etc.
I have downloaded some sequences from a publicly available database in .fa format. I want to generate a .csv file that contains the name of the sequence, and its length, separated by a comma.
This is ...
I have a long list of files named according to the following pattern:
Because these files correspond to different experimental ...
I recently linearized a fasta file, using awk. The ouput is perfect however the is a caret(^) in my sequence. I want to remove this caret. below is my attempt, any assistance is highly appreciated.
I am trying to install mamba through conda on my linux terminal on my chormebook. Please help. I need to install this for a final exmam. My professor just tells me look online. I am not a programmer ...
I have files molecule416_out.pdbqt, where I am using variable i (molecule$i_out.pdbqt) to loop over all files. But it looks like it is reading the variable as i_out instead of just i. Since all those ...
There are similar questions but none of them quite address the issue I have.
Simply put, I need to print every block that contains any string I'm looking for. Each block start line contains: <entry ...
I'm new to GNU sed (running on macOS) and wish to shorten some file headers (~50 K headers, 78.3 Mb).
I'm trying to modify FASTA files in place by specifying a backup extension with the -i flag.
I'm a beginner in bash scripting, can someone please help me here?
In a directory (pamlfiles/), I had list of files (*.fa)
The files look like this:
head -n 2 ....
I am trying to run FASTQC on some data. I am working on a server where I do not have root access. Does anyone know a way where I can install fastqc in my home space as I don't have root on the server ...
I have a sorted file of IDs and numbers (positions). I need to group the positions in the 2nd column into intervals of 500 in a group.
If the values of the row, when compared to the previous row are ...
Recently, I faced some problems in developing bash pipelines with docker.
This regards to the use of process substitution [<()] as input for a specific docker command.
I know that this is a problem ...
I want to grep exonic in my .tsv file provided that column 13 of this file contains p..
Can you help me with the code I need?
Note: As there are also exonic variants with no amino acid changes, I want ...
I have two files, file 1 and file 2. I want to suppose when the chromosome number are the same, if the second column in file 1 is greater than (the second column - 1,000) in file 2 and smaller than (...
I am using this command to grep the gene list in first file present in the gff file.
grep -w -f upregulated_genes_in_BEg GCA_900659725.1_ASM90065972v1_genomic.gff
it did not work for me.. please any ...
I have a file with this content:
I want to add new content to this file like:
I have a file like this:
I believe my problem is similar as found here but I was confused by the reply (and I can't comment in this question yet due to my low rep).
I have a bash script I need to run using slurm, so when the ...