SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
settings for the best hits in commandline blast kaps General 6 08-25-2016 07:33 AM
commandline blast kaps General 2 02-17-2015 01:17 AM
Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq on Galaxy lindseykelly RNA Sequencing 5 07-30-2014 01:09 PM
grooming fastq dots to N's Giles Bioinformatics 2 05-07-2012 02:36 AM
Illumina quality score encoding for galaxy grooming Mshegrss General 2 03-14-2012 06:53 AM

Reply
 
Thread Tools
Old 03-13-2015, 07:15 AM   #1
hyates
Member
 
Location: Kansas City

Join Date: Jan 2014
Posts: 18
Default How to perform grooming that galaxy does but on the commandline?

How do I groom sanger reads into sanger reads on my local commandline using the same tool that galaxy has found here?

In other words, I would like to do the following:
  • Obtain the same tool galaxy uses for grooming locally
  • Invoke this tool on my local commandline
  • Figure out how to use this tool on an entire directory of fastq files

I of course went to galaxy and I only saw a reference to a paper, but I don't know where to obtain the tool?

Thank you very much for reading this post.
hyates is offline   Reply With Quote
Old 03-13-2015, 07:21 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

There is no need to "groom" if your reads are already in sanger format.
GenoMax is offline   Reply With Quote
Old 03-13-2015, 07:28 AM   #3
hyates
Member
 
Location: Kansas City

Join Date: Jan 2014
Posts: 18
Default

Quote:
Originally Posted by GenoMax View Post
There is no need to "groom" if your reads are already in sanger format.
I am reading these notes and trying to duplicate the results. It states they used galaxy and the first step in the cleaning process was grooming. Specifically,
Quote:
Groomed 28403332 sanger reads into sanger reads
They then trimmed and then filtered the results. So what I should really be doing is focusing on the trimming and filtering, yes?

If so, my question is how can I obtain the tools galaxy uses for trim and filter for local commandline processing? Thank you for your patience and prompt answer.
hyates is offline   Reply With Quote
Old 03-13-2015, 07:36 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

You can get the code galaxy uses here (individual tools likely have other dependencies and it may not be simple to run them on the command line): https://toolshed.g2.bx.psu.edu/repos/devteam

As long as you know the reads are in sanger format (phred+33) you can go on to trimming/filtering.
GenoMax is offline   Reply With Quote
Old 03-13-2015, 07:54 AM   #5
hyates
Member
 
Location: Kansas City

Join Date: Jan 2014
Posts: 18
Default

Quote:
Originally Posted by GenoMax View Post
You can get the code galaxy uses here (individual tools likely have other dependencies and it may not be simple to run them on the command line): https://toolshed.g2.bx.psu.edu/repos/devteam

As long as you know the reads are in sanger format (phred+33) you can go on to trimming/filtering.
That's a great place to look. It would be nice if the tools had a readme.txt for dependencies, but I read whatever docs I can find first. If that doesn't work, I can always reach out again.

That being said, thank you so much Geno. You've been a lot of help and I want you to know this. Have a great day.
hyates is offline   Reply With Quote
Old 03-13-2015, 07:58 AM   #6
hyates
Member
 
Location: Kansas City

Join Date: Jan 2014
Posts: 18
Default

Quote:
Originally Posted by GenoMax View Post
As long as you know the reads are in sanger format (phred+33) you can go on to trimming/filtering.
Okay, my background is not biology and I am in computer science. So maybe you can answer this to me because the person who did this isn't here anymore.
  1. It seems the data is 100 cycle SE from high output: 1 lane (Illumina HiSeq 2500)
  2. They did trimming from sanger to sanger data?
  3. How can I verify myself that this is phred+33 format?

Did they make a mistake in grooming? It seems to me that Illumina HiSeq fastq data is not sanger? Or am I totally n00b?
hyates is offline   Reply With Quote
Old 03-13-2015, 08:13 AM   #7
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

Options for verifying phred+33 format: https://www.biostars.org/p/63225/

If your dataset is already sanger format then in galaxy it is possible to assign ".fastqsanger" type to this data avoiding the grooming step.
GenoMax is offline   Reply With Quote
Reply

Tags
commandline, fastq, galaxy, grooming, sanger

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO