SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie 2 explanation of the pair-end mode report wariobrega Bioinformatics 12 07-18-2018 10:57 PM
normalization of pair-end RNA-seq data with different sequence length yao_licr RNA Sequencing 1 04-21-2015 04:44 AM
Some "wrong" XS:A in Tophat output for strand specific pair-end RNA-Seq data ct586 Bioinformatics 4 05-08-2013 05:15 PM
75+35 Pair-end SOLiD RNA-seq data analysis endether SOLiD 11 12-12-2012 04:40 PM
What is this strand specific pair-end RNA-seq data? xhuister Bioinformatics 2 09-14-2010 06:34 AM

Reply
 
Thread Tools
Old 03-09-2016, 11:58 PM   #1
xuly
Junior Member
 
Location: China

Join Date: Mar 2016
Posts: 1
Unhappy what's wrong with the pair-end seq data if the fastqc report shows this patten?

I fsatqc the uniq-mapped reads, and the "Kmer content" showed a high repeat "CCCTACGTTCT" at the middle of the reads.

Is this means the error in the sequencing process?
Attached Images
File Type: png ??.PNG (129.0 KB, 22 views)
xuly is offline   Reply With Quote
Old 03-10-2016, 12:13 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Most likely, you just have a single sequence that's really really highly expressed. FastQC only shows 6 kmers in these sorts of graphs, so odds are good that there are other (not displayed) similarly enriched kmers on either side.

Alternatively, perhaps you were doing RIPseq and this is a binding motif (the fastQC results on such experiments looks similar).
dpryan is offline   Reply With Quote
Old 03-10-2016, 02:57 AM   #3
Ramet
Junior Member
 
Location: Germany

Join Date: Sep 2010
Posts: 9
Default

There seems to be something concatenated. Note the same order of peaks (red, green, black, blue, pink) in the middle and at the end of the sequence reads.

What are these data? Since they seem to be only 45 bp in length they are probably not freshly sequenced?!

Best,
Ramet
Ramet 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 05:41 AM.


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