SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to handle Ns in the middle of reads themysticgeek Bioinformatics 4 01-20-2014 04:27 AM
Trimming adapter sequence in the middle of a read milesgr Bioinformatics 7 12-15-2013 12:39 PM
Low quality in the middle of the read? MG1655 Illumina/Solexa 0 08-12-2012 12:22 PM
Hello from the middle of the USA smcinturf Introductions 0 07-25-2012 12:01 PM
K-mers charltt Bioinformatics 2 06-08-2011 11:03 AM

Reply
 
Thread Tools
Old 12-08-2015, 07:28 AM   #1
A-K
Junior Member
 
Location: London

Join Date: May 2015
Posts: 2
Default k-mers in the middle of the read

Hi All,

I'm new to RNASeq analysis and am looking for some advice on the FastQC k-mer output.

For several of my samples, I see accumulation of k-mers in the middle of the read. (see attached).

Does anyone have experience with this / know what the cause could be?

Your help is much appreciated,

A-K
Attached Images
File Type: jpg FASTQC_kmer.jpg (62.7 KB, 24 views)
A-K is offline   Reply With Quote
Old 12-08-2015, 07:34 AM   #2
asier_gonzalez
Junior Member
 
Location: Harpenden

Join Date: Dec 2015
Posts: 7
Default

Hey there,

If I'm not wrong, this probably means that there were many fragments that were shorter than 40-50 bp, that is, those overepresented sequences are probably the adaptors.

Let's see what more experienced people think.

Regards,

Asier
asier_gonzalez is offline   Reply With Quote
Old 12-08-2015, 08:48 AM   #3
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 503
Default

The over-represented sequence (CTCGTATGCCGT) is from the TruSeq index adapter (the segment immediately following the index). The spacing is consistent with adapter dimers. It appears that the data were trimmed, which removed the adapter sequences preceding the index but not those that followed.
HESmith is offline   Reply With Quote
Old 12-08-2015, 11:42 PM   #4
A-K
Junior Member
 
Location: London

Join Date: May 2015
Posts: 2
Default

Thanks both for the quick replies! Very helpful!
A-K is offline   Reply With Quote
Reply

Tags
fastqc, k-mer, middle, read

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 07:36 AM.


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