paired-end fastq file

Question

[evelyn]

Hello,

I am trying to find tools to calculate the read depth of paired-end fastq files. I am trying to downsample fastq files to 5x. I know I can subset using seqtk but I want to get a specific read depth (in my case 5x) for fastq file.

[GenoMax]

Read-depth for a fastq file is an odd concept. I assume you mean to get 1/5th of data or 5x based on genome size?

Have you tried reformat.sh from BBMap suite. Check the sampling parameters for in-line help.

If you are trying to normalize the data (rather than just downsample) then use bbnorm.sh. A guide for that is here.

[evelyn]

Thanks! I want to get 5x based on genome size. Like samtools depth can be used for bam/sam file, is there any tool for depth for fastq file. I have not used reformat.sh. Can you help provide the code.

[GenoMax]

reformat.sh is part of BBMap suite of tools. You can download them here.

You would likely use the following parameter:

samplebasestarget=0     (sbt) Exact number of OUTPUT bases desired.

reformat.sh in1=your_R1.fq.gz in2=your_R2.fq.gz out1=sample_R1.fq.gz out2=sample_R2.fq.gz samplebasestarget=N

N = 5 x your genome size.

[evelyn]

Thank you!!!!!!!!!