Question: paired-end fastq file
0
gravatar for evelyn
4 weeks ago by
evelyn30
evelyn30 wrote:

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.

sequencing • 105 views
ADD COMMENTlink written 4 weeks ago by evelyn30
1

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.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax69k

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.

ADD REPLYlink written 4 weeks ago by evelyn30

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.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax69k

Thank you!!!!!!!!!

ADD REPLYlink modified 27 days ago • written 4 weeks ago by evelyn30
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