NGS : merge fastq

Question

[quentin54520]

Hi all and sorry if my question has already been resolved. I am going to do all the bio info processing of my WGS for the first time so I obviously have some doubts, especially since it is sometimes difficult to know if what we did worked correctly or not. for each individual I have 8 fastq files. it's paired end so there are 4 R1 and 4 R2 files. I would like to know when and how should I merge them? if i merge the fastq i can do a cat file 1 2 3 4> newfile ? but if I merge the fastq to make a single R1 file and a single R2 file per individual is that information from which read is the mate of the other will be kept? because I would need this information for analyzes of structural variants.

Thanks in advance.

Answer 1

[Pierre Lindenbaum]

if i merge the fastq i can do a cat file 1 2 3 4> newfile ? but if I merge the fastq to make a single R1 file and a single R2 file per individual is that information from which read is the mate of the other will be kept?

concatenate the paired files in the very same order

cat fastq1.R1.fastq fastq2.R1.fastq fastq3.R1.fastq fastq4.R1.fastq > merged.R1.fastq
cat fastq1.R2.fastq fastq2.R2.fastq fastq3.R2.fastq fastq4.R2.fastq > merged.R2.fastq

see also: A: How To Merge Two Fastq.Gz Files?

because I would need this information for analyzes of structural variants.

in WES/WGS, most of the time, fastq files don't need to be concatenated. You map each pair of fastq in parallel and you later merge the bam files.

[quentin54520]

Thanks for your reply

I have 592 fastq files (74 individuals * 4 lanes * 2 ). so your recommendation is to leave those 592 files separate, do the alignment and merge the bams to get 74 bam? Because originally I intended to make 74 * 2 = 148 fastq files and start from there to do quality control, alignments.

[Pierre Lindenbaum]

so your recommendation is to leave those 592 files separate, do the alignment and merge the bams to get 74 bam?

yes

Because originally I intended to make 74 * 2 = 148 fastq files

you can always do that for QC . But anyway, if the fastqs come from 4 lanes, one want to get a QC per lane/sample.