SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
NGS Data Analysis Workshop & Conference: NGS 2017 Glasgow (15-16 May) Biotexcel Events / Conferences 0 02-09-2017 10:11 AM
Upcoming NGS Workshop: A Beginner's Guide to NGS Data Analysis (early march 2015) ecSeq Bioinformatics Clinical Sequencing 1 06-29-2015 07:31 AM
Upcoming NGS Workshop: A Beginner's Guide to NGS Data Analysis (early march 2015) ecSeq Bioinformatics Bioinformatics 1 01-15-2015 01:35 AM
Webinar on Methyl Seq data analysis in Strand NGS- Formerly Avadis NGS Strandlife Events / Conferences 1 10-21-2014 02:28 AM
Looking for a few NGS-ers willing to share a bad experience about NGS data analysis CHoyt Bioinformatics 8 12-09-2011 11:06 PM

Reply
 
Thread Tools
Old 03-31-2018, 07:47 AM   #1
pablo12
Junior Member
 
Location: Europe

Join Date: Mar 2018
Posts: 1
Default NGS-Ig data

Dear users,

I'd like to ask you for your advise on a certain project that I am working on.

My job is to retrospectively analyse NGS data from patients suffering from ALL and MM (IGH).
However, I am not a bioinformatician. I just received the sequencing data in Excel (and .csv) files and I'm supposed to analyse these data.

Of course, I've heard of IMGT/VQUEST and IgBlast and it is no problem for me to work with these programmes. But the issue is that I can't do this with tens of thousands of sequences.

After further research, I came across the R tool tcR. It seems to be a well-done programme. Unfortunately, I always receive error messages when trying to integrate my files in it.

I found out that it might be useful to convert my files into .txt files or to work with VDJ-tools, Immunoseq, mixcr or other tools. But I do not have access to these programmes or they require Linux (which I don't have; Windows).

In addition, the sequencing data in my Excel files are not in fasta-format. But if I would change this by editing the sequences manually I'd be busy for the next three months.

My goal is to analyse my data for gene usage and to be able to search quickly for potential subclones.


I look forward to hearing your opinion!
Thanks in advance!

Pablo

Last edited by pablo12; 03-31-2018 at 08:00 AM.
pablo12 is offline   Reply With Quote
Old 04-16-2018, 05:49 AM   #2
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 401
Default

You can probably use the sequences from the CSV files to create fasta files with a bit of creativity.

Have a look at good text editors like Notepad++ to get this done.

Also check out Galaxy for user friendly processing tools.
colindaven is offline   Reply With Quote
Reply

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 12:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO