Question: Difference between Fastq and Fastqsanger?
0
gravatar for krishnakarthik.vemuri
2.6 years ago by
krishnakarthik.vemuri10 wrote:

Hi, 

Can somebody briefly explain the difference between fastq and fastqsanger files in Galaxy? I have tried to download fastq files from an experiment using the EBI SRA tool, and tried to run Tophat on them to get BAM files for further analysis, but in the Tophat tool, I get a message saying no fastqsanger files available. I am not able to understand this. If somebody can point me towards a reference for this, I would be very grateful.

K

 

ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson23k • written 2.6 years ago by krishnakarthik.vemuri10
1
gravatar for Martin Čech
2.6 years ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

These are different types of fastq data. Use the tool fastqGroomer to change their type.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Martin Čech ♦♦ 4.2k
1
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Martin is correct. I'll add just a little more info in case you need some more background and/or an example of using this tool or fastq formats in general. The Galaxy wiki has a section about this datatype: FASTQ Datatype QA

The video explains much in detail and the link you will find to wikipedia is a great resource for more information concerning legacy fastq formats.

Take care, Jen, Galaxy team

ADD COMMENTlink modified 2.6 years ago by Martin Čech ♦♦ 4.2k • written 2.6 years 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: 101 users visited in the last hour