SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Adapter trimming figo1019 RNA Sequencing 2 07-17-2018 04:00 AM
Best adapter trimming? ronton Bioinformatics 12 08-21-2014 03:04 PM
Adapter trimming and trimming by quality question alisrpp Bioinformatics 5 04-08-2013 04:55 PM
adapter trimming - help a_mt Bioinformatics 6 11-12-2012 07:36 PM
3' Adapter Trimming caddymob Bioinformatics 0 05-27-2009 12:53 PM

Reply
 
Thread Tools
Old 07-05-2018, 07:10 AM   #1
HarshJ
Junior Member
 
Location: India

Join Date: Jul 2018
Posts: 2
Post Stuck at adapter trimming

Hi!

So, I'm trying to analyse and subsequently map the data deposited with the following paper:

http://science.sciencemag.org/conten...3/aah5651.full

I have downloaded and 'fastq-dump'ed the ChIP-Seq files and have also run a fastqc for quality scores. Now as these reads are raw, they still need adapter trimming and filtering. However, I am unable to figure out what adapter sequence to use for trimming.

I am putting up this question here because the paper states,
Quote:
Libraries for ChIP-seq were constructed using the NEBNext ChIP-seq kit (New England Biolabs), barcoded, multiplexed, and sequenced on an Illumina MiSeq with a paired-end run type

Help!
HarshJ is offline   Reply With Quote
Old 07-05-2018, 10:16 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,780
Default

You can find the NEBnext adapter sequences in this manual.
GenoMax is offline   Reply With Quote
Old 07-06-2018, 12:36 AM   #3
fkrueger
Senior Member
 
Location: Cambridge, UK

Join Date: Sep 2009
Posts: 606
Default

You should be able to use Trim Galore for this which will try to identify the adapter sequence for you. The command for adapter and quality trimming is simply:

Code:
trim_galore --paired file1 file2
fkrueger is offline   Reply With Quote
Reply

Tags
chip-seq analysis, cutadapt, illumina

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 04:23 AM.


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