extraction of last 400 nucleotide from fastq file using python
0
0
Entering edit mode
3.3 years ago
vaishnavi ▴ 80

Hi everyone,

I want to extract the last 400 sequence from a fastq file using python, I am a beginner in bioinformatics can anyone please guide me how to do it?

Python fastq • 1.3k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

I appreciate your suggestion but I need to extract sequence from a illumina based file which has a fastq format.

ADD REPLY
0
Entering edit mode

If you have raw Illumina data then you don't have any reads that are longer than 150/300 bp long (disclaimer: it is possible to run a paired-end 300 bp kit as single end to get 600 bp reads but that would be highly unusual/non-standard).

If you don't have raw data then your reads are no longer in fastq format. So please clarify exactly what you have and what you want to get out of that data.

ADD REPLY
0
Entering edit mode

I want extract last 400 reads from a fastq file, containing 72 bp per read using linux command.

ADD REPLY
1
Entering edit mode

I want extract last 400 reads from a fastq file

This is a completely different requirement than what the title of the post says.

You can do this reformat.sh in=your.fq out=sampled.fq skipreads=N (from BBMap Suite). Set N = (total reads - 400).

Note: If this is an assignment and requires you to specifically use python then please make a note of that. You will also need to show some code you wrote for people to provide suggestions.

ADD REPLY
0
Entering edit mode

thankyou for help, this was an assignment it was suppose to be done in python but my professor changed it to linux now.

ADD REPLY

Login before adding your answer.

Traffic: 1741 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