How get read group information from fastq files in SRA

Question

[zamani_2012]

Hi everyone, I want to align some paired fastq files to canine reference genome using BWA-MEM tool. I downloaded fastq files from SRA. I need to specify read group information using -R option in BWA-MEM. I dont have such information. How can I access to read group information for each fastq file? Are these information available in SRA? any help will be greatly appreciated?

Answer 1

[ATpoint]

This option is not mandatory, just leave it blank. There is no formal definition of a read group, therefore this information is not in the SRA. Only some tools like GATK actually require it.

[zamani_2012]

Many thanks for your comment. If I do not enter this information, will it not have a negative effect on subsequent analyzes? I work on WGS data and I use GATK for variant calling.

[GenoMax]

If you are going to use GATK then you will have to use read groups. You can make up basic RG information based on type of sample you are working with.