Question: paired-end fastq file
0
gravatar for evelyn
11 months ago by
evelyn90
evelyn90 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 • 203 views
ADD COMMENTlink written 11 months ago by evelyn90
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 11 months ago • written 11 months ago by genomax83k

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 11 months ago by evelyn90

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 11 months ago • written 11 months ago by genomax83k

Thank you!!!!!!!!!

ADD REPLYlink modified 11 months ago • written 11 months ago by evelyn90
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