fastq file split in chromosome

Question: fastq file split in chromosome

2.2 years ago by

im newbie to NGS and linux. can anyone kindly let me know the easiest way to split the fasta file containing chromosome and scaffold into individual files i.e files containing one chromosome per file... thanks

next-gen • 993 views

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modified 2.2 years ago by Bastien Hervé ♦ 4.6k • written 2.2 years ago by blooming.daisy333 • 90

How do you know which scaffold belongs to which chromosome ? If you don't, you'll have to align all your scaffolds on a reference genome. If you have the information in your scaffold headers, you can split your file with a python script for example.

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by Bastien Hervé ♦ 4.6k

sorry it was about Fasta file containing genome sequence and not fastq. i need each chromosome to be in single seperate file rather to be all the genome in one fasta file. any help plz???

ADD REPLY • link written 2.2 years ago by blooming.daisy333 • 90

Aah, I got it, you have a reference genome in fasta and you want to split each sequence to a separated file, isn't it ?

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by Bastien Hervé ♦ 4.6k

Please follow up on your previous threads and mark answers as accepted when appropriate.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLY • link written 2.2 years ago by WouterDeCoster ♦ 44k

2.2 years ago by

Bastien Hervé ♦ 4.6k

Karolinska Institutet, Sweden

Bastien Hervé ♦ 4.6k wrote:

A modification of Pierre's answer from here : Splitting A Fasta File

awk '/^>/ {F=substr($0, 2, length($0))".fasta"; print >F;next;} {print >> F;}' < ref_genome.fasta

Just replace ref_genome.fasta with your file

ADD COMMENT • link modified 2.2 years ago • written 2.2 years ago by Bastien Hervé ♦ 4.6k

2.2 years ago by

Bastien Hervé ♦ 4.6k

Karolinska Institutet, Sweden

Bastien Hervé ♦ 4.6k wrote:

I think you could have found this answer somewhere in Biostars, like this one :

How to split fasta into seperate files by chromosome (in the header)

If I understand correctly your goal :

from Bio import SeqIO

for record in SeqIO.parse('ref_genome.fasta', 'fasta') :
    with open( record.id+".fasta", "a") as output_handle :
        SeqIO.write(record, output_handle, 'fasta')

ADD COMMENT • link modified 2.2 years ago • written 2.2 years ago by Bastien Hervé ♦ 4.6k

yes you ve correctly guessed the requirement. thanks for the answer. but is there any other one iiner command like csplit awk ets. I am newbie to linux and could not understand the above command

ADD REPLY • link written 2.2 years ago by blooming.daisy333 • 90

It's not a unix command, it's python code.

ADD REPLY • link written 2.2 years ago by WouterDeCoster ♦ 44k

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