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How get read group information from fastq files in SRA

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?

read group fastq sra bwa
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updated by ATpoint ATpoint • written by zamani_2012 • zamani_2012

1 answer

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.

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written by ATpoint ATpoint

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.

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written by zamani_2012 • zamani_2012

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.

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written by GenoMax GenoMax

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