Question: How get read group information from fastq files in SRA
0
gravatar for zamani_2012
4 weeks ago by
zamani_20120 wrote:

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?

bwa read group fastq sra • 122 views
ADD COMMENTlink modified 4 weeks ago by ATpoint40k • written 4 weeks ago by zamani_20120
0
gravatar for ATpoint
4 weeks ago by
ATpoint40k
Germany
ATpoint40k wrote:

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.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by ATpoint40k

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.

ADD REPLYlink written 4 weeks ago by zamani_20120

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.

ADD REPLYlink written 4 weeks ago by genomax91k
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