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Using shells other than bash

Bioinformatics tools written in shell and other shell scripts generally specify the shell they want to use (via #!/bin/sh or e.g. ...

Using shells other than bash

TL;DR SH adheres to an official industry standard, but it is not suitable for scientific computing. Bash is considered an informal standard (e.g., by Google). Bash 3 is preferable in most of ...
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• 3,472
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Batch alignment of inconsistently named Fastq files

A very simple approach, but one which will work with the names you show, is to remove any occurrence of 00N (where N is any ...
• 7,957

How to merge .fastq.qz files into a single .fastq.gz with their same id without losing any content in parallel

We sequence DNA on daily basis. Like terdon said, you can use cat to group all the FastQ of all your sample whether they are ...
• 968
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Using a Bash Script to search TaxIDs against NCBI's Taxonomy yields "400 Bad Request" error?

If I understand correctly, your question boils down to: parsing a bunch of numbers in a row from a .csv file gives a different result from parsing a bunch of numbers as rows of a text file. I that ...
• 258

Replace lowercase characters with -

You could try it with sed. Replace all lower-case chars with - in lines not starting with ...
• 423

Remove/delete sequences by ID from multifasta

Using the FastaToTbl and TblToFasta scripts I have posted before, you can do: ...
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How I can change the name of multiple files at once in R or terminal?

If your filenames do not contain blank spaces, you can do it with a for-loop in bash: Make a test run with echo so that the ...
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