18 results in 0.0021 seconds.
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shournal: A Tool for Bioinformaticians to Boost Research Reproducibility
I recently stumbled upon a fascinating paper about "shournal," a tool designed for bioinformaticians! It's a game-changer for enhancing reproducibility...
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bash loop to count multiple words from multiple corresponding files
I have generated multiple read mapping files (.sam) generated with bowtie2 "--no-unal" parameter. As the number of files are huge (7 reference... -
Multiple fastq alignment with bowtie2 in server
Hi!
I'm trying to map multiple sra files (>6500) with bowtie2 against my reference genome. I am running slurm script in a server. While mapping... -
Bash Error "Unexpected token near done"
Hi!
I wrote the following little bash script:
...Code:echo Processing... inputDir="/home/j490h/localhome/fastq/"
Last edited by GenoMax; 04-02-2019, 11:26 AM. -
Read in script
Hi all,
I want to write a bash script that reads in a file and performs several processing steps with that input file.
Can... -
Hisat2: no command found in bash
Hi all,
I'm a complete novice at RNAseq mapping and I am trying to follow this protocol using their data: https://www.nature.com/nprot/journal... -
Error when using SRA toolkit on server
Hello everyone,
I am having a bit of a problem using the SRA toolkit on the external server i use. I've downloaded it using the command... -
Bash script to automate htseq-count
Hi everyone-
I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following... -
Doing local blast. No alias or index file found for nucleotide database?
I am attempting to do a local blast nt. I have implemented the following procedure:- update_blast.pl nt
- tar zvpf nt.01.tar.gz command for each volume
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How can I write a bash command to blast local nt database?
I have been reading this.
I was able to write a basic query using blast n as follows:
...Code:blastn -db ~/programming/blastexample/db/tdb
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awk/bash/perl/sed one-liners explained
I landed on this website by accident. After a little browsing, I just felt like I had to share it here. Any good bioinformatician should be at least somewhat... -
parsing the gff file
Hi all,
I have a gff file like:
gn|nvit|C3905550 assmcg CDS 68 646 . - . asmbl_401
...Last edited by Shishir; 09-06-2013, 03:48 AM. -
Copy the column and paste it with special character
Hi all,
I have a input file like
C3905550 oder CDS 68 646 . - . asmbl_487
C3905550... -
Extracting the pattern not matching
Hi there,
I have a list of sequence id and I am trying to extract the sequences from the proteome of the organism using these ids. I used... -
annovar output problems
Hi,
I have trouble making Annovar’s gene annotation tool work well.
I am working on a virus, so had to build the reference...
