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 11:11 AM
Upcoming NGS Workshop: A Beginner's Guide to NGS Data Analysis (early march 2015) ecSeq Bioinformatics Clinical Sequencing 1 06-29-2015 08:31 AM
Upcoming NGS Workshop: A Beginner's Guide to NGS Data Analysis (early march 2015) ecSeq Bioinformatics Bioinformatics 1 01-15-2015 02:35 AM
Webinar on Methyl Seq data analysis in Strand NGS- Formerly Avadis NGS Strandlife Events / Conferences 1 10-21-2014 03:28 AM
Looking for a few NGS-ers willing to share a bad experience about NGS data analysis CHoyt Bioinformatics 8 12-10-2011 12:06 AM

Reply
 
Thread Tools
Old 11-16-2020, 01:26 AM   #1
Marko Radojkovic
Junior Member
 
Location: Netherlands

Join Date: Nov 2020
Posts: 1
Default NGS data analysis - help

Hello everyone!

I am a 1st year PhD Biochemistry student who is doing NGS for the first time (also the first time in our research group).

Long-story short: We have two mutant libraries (484 and 1024 unique clones), both having two different barcodes and we are planning to pool them and sequence together. PCR amplicons will be 180 bp long, and they will only differ in 6 bp which is in the middle of the sequence.

Sequencing will be done on Illumina platform, here are the specs:
- Technology: Illumina NovaSeq
- Run type: Paired end
- Read length: 2 x 150 bp
- Guaranteed 5 million read pairs (10 million reads) per package (+/- 3%)
- Guaranteed 1.5 Gb raw data per package (+/- 3%)
Deliverables: FastQ Files (sequences and quality scores)

Since I am doing this for the first time, I have no experience in data analysis.
I would like to do basic things: merging of overlapping reads, tag sorting and counting/calculating percentage of each variant. If anyone can recommend me software for data analysis, which is suitable for inexperienced user like me, to run on Windows preferably, but Linux would also work.

If you have any other advice/recommendation it will be more than welcome!

Thank you.

Best regards
Marko Radojkovic is offline   Reply With Quote
Reply

Tags
illumina fastq, novaseq, paired-end reads

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 11:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO