Question: Using BWA-MEM to align fastq files from MinION
0
gravatar for christopher.phiel
7 months ago by
christopher.phiel0 wrote:

I am trying to use BWA-MEM in Galaxy to align fastq files to mouse genome. I am having an issue with selecting the fastq dataset option. All fastq files have been uploaded to my history. How do I get the workflow to recognize these files?

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson23k • written 7 months ago by christopher.phiel0

ADD REPLYlink modified 3 months ago • written 3 months ago by renae.geier40
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The datatype needs to be confirmed to be in Sanger Phred +33 format (or rescaled to that format) then assigned the .fastqsanger datatype.

How to: https://galaxyproject.org/support/#getting-inputs-right- >> How to format fastq data for tools that require .fastqsanger format?

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson23k

Hi Jen, thanks for pointing me in the right direction. When I go to the Fastq Groomer function, I need to select the correct quality scores type, but there are only 4 listed and none of them is for Nanopore sequencing. Any idea what I should select? Just trying each one failed to have the command executed.

ADD REPLYlink written 7 months ago by christopher.phiel0

Hi Jen, I figured it out.

ADD REPLYlink written 7 months ago by christopher.phiel0

Christopher, Thanks for updating and glad you were able to sort this out! - Jen

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson23k

Fastq data extracted from this data should already be in fastqsanger format, which means that the datatype .fastqsanger can be directly applied (no need to groom to transform quality score values).

But it is a good practice to check. Did the FastQC report guess that the (quality score) encoding was something other than "Sanger/Illumina 1.9"?

ADD REPLYlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 117 users visited in the last hour