Filtering 50 biggest contigs
0
0
Entering edit mode
3.9 years ago
stan.aanhane ▴ 30

Hi everyone,

After performing a novo assembly, with the followed command, i want to filter the biggest 50 contigs.

spades.py --untrusted-contigs lclav_genome.fa -1 randomnietnfectedFP.fastq.gz -2 randomnietinfectedRP.fastq.gz -t 2 -m 28 NINnovo --phred-offset 33

This creates a directory with the contigs in it. This file is sorted from biggest to smallest, and we want just the top 50 of these contigs. I have tried something with awk, but it is not working how i want it to. CAn someone help me out?

Thank you!

Novo linux • 940 views
ADD COMMENT
1
Entering edit mode

You could convert multiline fasta to single line using Multiline Fasta To Single Line Fasta and then extract the first 100 lines using head which should extract the top 50 contigs for you.

ADD REPLY
0
Entering edit mode

Don't forget to change them back to fasta format.

ADD REPLY
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 2103 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6