Question: Extracting a special chromosome in fastq file
gravatar for Sakhaa
4 weeks ago by
Sakhaa0 wrote:


I'm a beginner in bioinformatic filed and I want to extract chr.22 from the fastq file. I don't know which tool should I use. Could anyone help me in that?

Thank you

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Sakhaa0

Hello and welcome to biostars Sakhaa ,

fastq files doesn't contain any information about the origin of the reads. You first have to align those reads to the genome resulting in a bam file. From there you can extract anything specific for a chromosome.

fin swimmer

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by finswimmer11k

Fastq file contains reads from all the complete genome (at least you sequenced chr22), therefore, you have to align reads against the genome to clasify them by its corresponding genome location, then you can extract reads of your interest. 1.- Read about bowtie2 to align your sequences. 2.- Read about sam/bam files samtools (result of bowtie2 aligner) and how to extract data from specific location.

ADD REPLYlink written 4 weeks ago by Buffo1.4k

Is it a fasta or fastq? head your.file please. If fasta:

>name of sequence
>name of next sequence
next sequence

then use samtools faidx. Details via google and the search function. Asked many times before, e .g. Filtering Fasta Sequences By Chromosomes Names From A Big Fasta File

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by ATpoint14k
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