Entering edit mode
4.8 years ago
evelyn
▴
220
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.
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.Thanks! I want to get 5x based on genome size. Like
samtools depth
can be used forbam/sam
file, is there any tool for depth for fastq file. I have not usedreformat.sh
. Can you help provide the code.reformat.sh
is part of BBMap suite of tools. You can download them here.You would likely use the following parameter:
N = 5 x your genome size.
Thank you!!!!!!!!!