Paired-end SRA files t Fastq Files

0

Entering edit mode

2.5 years ago

Umer ▴ 50

Hey Reader,

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.

ncbi analysis sequence sra next fastq-dump generation • 918 views

ADD COMMENT • link updated 2.5 years ago by GenoMax 141k • written 2.5 years ago by Umer ▴ 50

1

Entering edit mode

2 ABI_SOLID (AB SOLiD System 3.0)

This is color-space data. Stay away if you can. Probably not worth the hassle of dealing with this type of data.

ADD REPLY • link 2.5 years ago by GenoMax 141k

0

Entering edit mode

How did you find out the data type that its color space ?

ADD REPLY • link 2.5 years ago by Umer ▴ 50

1

Entering edit mode

That information is in the SRA accession record.

ADD REPLY • link 2.5 years ago by GenoMax 141k

Login before adding your answer.