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Question: Extract reads in FASTQ/A format from NCBI SRA
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gravatar for planetypus
21 months ago by
planetypus • 0
planetypus • 0 wrote:

Hi. I downloaded an SRA accession. In the results, the spots were separated but is in the same file. How can I separate each read into a separate fastq file? Thank you.

Is there a way to extract them straight from SRA and have outputs of forward and reverse files?
rna-seq software error galaxy assembly • 1.6k views
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modified 20 months ago • written 21 months ago by planetypus • 0
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool extracts the data in the format the data source servers, which in this case can be merged paired-end files.

For many use cases, this is the general prep workflow for fastq reads from NCBI:

  1. Get fastq data into Galaxy using NCBI SRA Tools > Extract reads
  2. Rename sequences - do this if the quality score labels on the "+" lines differ from the sequence names on the "@" lines
  3. FASTQ splitter
  4. FastQC
  5. Fastq Groomer or assign datatype to "fastqsanger" directly if quality scores already scaled for this format
  6. FastQC on the entire dataset again, if the Fastq Groomer was used
  7. Trim/filter as needed
  8. Downstream tools

Thanks!
ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Hi, Jennifer.

When I downloaded the reads from SRA, I split spot by read pairs, so the output is a file with interlaced read pairs, as the figure below shows. However, I want to separate these two paired-end reads into separate files. Is there any method to do that in galaxy? Thank you.

enter image description here

ADD REPLY • link modified 20 months ago • written 20 months ago by planetypus • 0

I think I should change something in the parameter when dumping the fastq file from SRA. Can you please suggest something I need to change based on the parameters below?

enter image description here

ADD REPLY • link modified 20 months ago • written 20 months ago by planetypus • 0
0
gravatar for planetypus
20 months ago by
planetypus • 0
planetypus • 0 wrote:

Thank you, Jennifer. I am trying to follow your workflow now. I will let you know about the outcome. I appreciate it!
ADD COMMENT • link written 20 months ago by planetypus • 0
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