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8 votes
7 answers
2k views

What are the available cloud computing services for bioinformatics? [closed]

I'm looking for cloud computing services that can be used for doing bioinformatics. An example I found is InsideDNA and there is Amazon of course. A little description of these would be appreciated.
Peter's user avatar
  • 2,634
3 votes
2 answers
683 views

How to remove sequences from a fasta file using a sequence ID list which contains a space within the id?

I have a fasta file that contains sequence reads and sequence id file that needed to be removed from the fasta file. I have done this earlier, but since id contains a space my piece of code is not ...
MudithMMBc's user avatar
3 votes
3 answers
149 views

How to get the product of a CDS

I need the name of the protein in /product="protein_name" using bash commands. Beware, there is a lot of whitespace between lines. ...
Aron van Beelen's user avatar
1 vote
1 answer
152 views

How to use Gblocks for trimming single-copy gene sequences?

I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
K_081's user avatar
  • 149
0 votes
2 answers
202 views

Changing this code in a way to work for my files

I have a bash script which extracts some information from a .vcf file but one .vcf file at each time. How I can change this script in a way to work on a bunch of .vcf files and the output is a .txt ...
Zizogolu's user avatar
  • 2,160
0 votes
2 answers
215 views

Looping over several files in bash

I have a bash script: I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf I tried changes done in similar script ...
Zizogolu's user avatar
  • 2,160