Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Adapter and quality trimming using Trim Galore integrated Galaxy
0
gravatar for evensky.maria
2.4 years ago by
evensky.maria • 0
evensky.maria • 0 wrote:

Hello. I need to make adapter trimming and quality trimming for my FASTQ paired files. I work in the operating system Windows 8 thats why I decided to do it using Trim Galore in GALAXY. I registered here https://usegalaxy.org and I choosed "NGS: QC and manipulation" -> "Trim Galore". But how to proceed, I can't understand. Please tell me. It requires downloading files (possibly, gz-archives)? but they are of great size.

Kind regards, Maria.
fastq trim galore galaxy paired trimming • 1.3k views
ADD COMMENT • link •
modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by evensky.maria • 0
0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Inputs to the tool can be uploaded, even large files (up to 50 GB). Use the FTP method defined here: https://wiki.galaxyproject.org/Support#Loading_data

Fastq data should be properly prepared and have the correct "datatype" assignment. This is how: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

More about NGS data in general is covered in detail in this tutorial: https://github.com/nekrut/galaxy/wiki/Introduction-to-NGS-technologies

For usage, the underlying tool binary's manual (linked from the tool form) defines the tool functions. The wrapped Galaxy tool implements most of these.

After reviewing, if there is a specific option/function you are not sure about, we can help.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

hi jen i request you to please elaborate on trimming by using trimmomatic. i am working on single end NGS data. i got 60 percent mapping after trimming by trim galore so wanted to switch over to some other trimming method for improving the mapping. i requet you to pleae guide me and help me to do the same. i have read the paper also on trimmomatic. but what exactly parameters i should set i request you to help. thanks

ADD REPLY • link written 2.1 years ago by 1603.neha • 70
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: 181 users visited in the last hour