SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
High amounts of Kmer at the 3' end after Trimming Zapages RNA Sequencing 15 04-13-2014 01:33 PM
strange FastQC kmer plot even after trimming fahmida Bioinformatics 8 08-01-2013 11:23 PM
Adapter trimming and trimming by quality question alisrpp Bioinformatics 5 04-08-2013 05:55 PM
Please Help: What is the differences between standard trimming and adaptive trimming byou678 Bioinformatics 8 08-22-2011 01:05 PM
optimal Kmer PHSchi Bioinformatics 0 02-16-2011 12:30 PM

Reply
 
Thread Tools
Old 07-07-2014, 02:43 PM   #1
Alex Lee
Junior Member
 
Location: N. Cal

Join Date: Apr 2014
Posts: 10
Smile Kmer changes after Trimming

Hi All,
I'm getting higher Kmers on my 5' end after trimming with trimmomatic-0.32. My samples are paired RNA-Seq from Illumina Miseq. I'm using FastQC Report to detect overrepresentation of Kmers. My original untrimmed samples show a high overrepresentation of Kmers on my 3í end but after trimming its now on the opposite side. The command that I used is the following.

java -jar trimmomatic-0.32.jar PE -phred33 -trimlog log.txt F.fastq R.fastq f_m.fastq f_um.fastq r_m.fastq r_um.fastq ILLUMINACLIP:all.fa.fa:2:30:5:2:true LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36 TOPHRED33

Iím using a custom adapter file called all.fa. I made 3 pdf to show before, after and the custom adapter files. Iím doing something wrong but can't figure out what. Thanks in advance.
Attached Files
File Type: pdf before_trimm.pdf (328.2 KB, 44 views)
File Type: pdf after_trimm.pdf (393.7 KB, 11 views)
File Type: pdf all.fa.pdf (89.3 KB, 5 views)
Alex Lee is offline   Reply With Quote
Old 07-07-2014, 03:29 PM   #2
Bukowski
Senior Member
 
Location: UK

Join Date: Jan 2010
Posts: 390
Default

This really needs to be a FAQ item on here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896536/
Bukowski is offline   Reply With Quote
Reply

Tags
rna sequencing, trim adapter, trimming, trimmomatic

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 07:13 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO