This might seem like a pretty nieve question. Kindly help me with this. I've downloaded whole cattle genome from NCBI accession number "SRX195354". As per my understanding it is a paired-end data for Holstein goldwyn cattle. Questions i want to ask are
- Is this really paired-end data? both files with accession numbers SRR592656 and SRR592657 represent the Forward and Reverse data ?
- How to convert these SRR files to fastq file? I've used fastq-dump without specifying any parameters on both SRR files to obtain fastq files.
- Running FastQC on both fastq files shows that the reads are of really bad quality ( below 20 scores ). Am I missing any specific way of dumping fastq data from SRR files.
Any help will be greatly helpful for me in this regard. THank You.