Question: Extract reads in FASTQ/A format from NCBI SRA
0
gravatar for planetypus
18 months ago by
planetypus0
planetypus0 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?

ADD COMMENTlink modified 18 months ago • written 18 months ago by planetypus0
2
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k

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 REPLYlink modified 18 months ago • written 18 months ago by planetypus0

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 REPLYlink modified 18 months ago • written 18 months ago by planetypus0
0
gravatar for planetypus
18 months ago by
planetypus0
planetypus0 wrote:

Thank you, Jennifer. I am trying to follow your workflow now. I will let you know about the outcome. I appreciate it!

ADD COMMENTlink written 18 months ago by planetypus0
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