Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Using BWA-MEM to align fastq files from MinION
0
gravatar for christopher.phiel
18 months ago by
christopher.phiel • 0
christopher.phiel • 0 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?
fastq bwa-mem bwa datatype fastqsanger • 1.1k views
ADD COMMENT • link •
modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by christopher.phiel • 0

ADD REPLY • link modified 14 months ago • written 14 months ago by renae.geier • 40
0
gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 18 months ago by christopher.phiel • 0

Hi Jen, I figured it out.

ADD REPLY • link written 18 months ago by christopher.phiel • 0

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

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link modified 18 months ago • written 18 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour