How to filter seqs by their 1st nt

cascoamarillo · 08-18-2011, 07:53 AM

Hi,

It sounds silly, but I couldn't find an approach for filter/separate sequences (in a fasta file) according to their first (or specific motif) nucleotide; I mean, to generate a file of seqs that starts all of them with the same nucleotide (A, T, G or C). Any ideas?

regards

NicoBxl · 08-18-2011, 11:42 PM

simple with cat and grep :

here's the code to filter only the sequences that start with an A. For the other nt, juste change the A into T,G or C. The only thing, it's that each sequence must be written in one line. Fasta Width from galaxy do that (http://main.g2.bx.psu.edu/) Fasta Manipulation > Fasta Width.

Quote:

cat input.fasta | grep ^A -B 1 | grep '\-\-' -v > output.fasta

cascoamarillo · 08-19-2011, 06:40 AM

Thanks mate!

It works fine.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
DGE - filter or not filter	masterpiece	Bioinformatics	0	07-11-2011 08:55 PM
Our new HiSeq, 1st impressions...	james hadfield	Illumina/Solexa	20	02-22-2011 05:48 AM
1st Galaxy Developer Conference \| CSHL	nekrut	Events / Conferences	0	01-19-2010 06:02 AM
1st Cycle Int (PF)	wouter	Illumina/Solexa	8	10-06-2009 11:22 PM
1st cycle report	bioinfosm	Illumina/Solexa	11	10-10-2008 06:13 AM

08-18-2011, 07:53 AM	#1
cascoamarillo Senior Member Location: MA Join Date: Oct 2010 Posts: 160	How to filter seqs by their 1st nt Hi, It sounds silly, but I couldn't find an approach for filter/separate sequences (in a fasta file) according to their first (or specific motif) nucleotide; I mean, to generate a file of seqs that starts all of them with the same nucleotide (A, T, G or C). Any ideas? regards

08-19-2011, 06:40 AM	#3
cascoamarillo Senior Member Location: MA Join Date: Oct 2010 Posts: 160	Thanks mate! It works fine.