How to merge multiple paired fastq files using BBmerge?

Question

[Princy]

Hello, I need to run Spades, i have WGS 230 paired end fastq files. First, I want to merge my R1.fastq and R2.fastq files into merge_R1.fastq and merge_R2.fastq . Pls, let me know how can I merge using bbmerge tool.

bbmerge.sh in1=<read1> in2=<read2> out=<merged reads> outu1=<unmerged1> outu2=<unmerged2>

Answer 1

[shelkmike]

Probably, you misunderstand what read merging is. There are two different types of merging (when you overlap reads by their ends, or when you just combine two files with reads into one), and none of them result in "merge_R1.fastq" and "merge_R2.fastq" files. Also, Spades does not require reads to be merged, whatever you mean by merging.

Bbmerge overlaps reads by their ends. You can use a command like:

bbmerge.sh in1=reads_R1.fastq in2=reads_R1.fastq out=merged.fastq outu1=unmerged_R1.fastq outu2=unmerged_R2.fastq ihist=ihist.txt

[GenoMax]

Bbmerge overlaps reads by their ends.

Only if they actually overlap. Like below

R1 --------------------------->
                       <------------------------- R2