Paired-end SRA files t Fastq Files
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5 weeks ago
Umer • 0

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

  1. Is this really paired-end data? both files with accession numbers SRR592656 and SRR592657 represent the Forward and Reverse data ?
  2. 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.
  3. 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 • 230 views
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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.

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

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That information is in the SRA accession record.

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