SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Wrong number of mapped reads in TopHat2 output Mchicken Bioinformatics 0 04-28-2015 01:36 AM
Confusion about single end vs paired end read output on Illumina HiSeq acidcoated Illumina/Solexa 1 03-19-2015 08:56 AM
Tophat2 read-gap-length and read-mismatches max acceptable values ElizabethRoss RNA Sequencing 0 10-13-2014 03:38 PM
TopHat2 failed to read known junctions from GTF file (from ensembl or UCSC) Alex234 RNA Sequencing 4 08-05-2013 08:31 AM
tophat2/bowtie2 inconsistency in number of unmapped reads manianslab Bioinformatics 2 07-13-2012 12:56 PM

Reply
 
Thread Tools
Old 07-24-2015, 04:45 AM   #1
abisko00
Member
 
Location: Munich

Join Date: Jul 2015
Posts: 14
Default Read number confusion in tophat2

Dear all,

I am very new to RNA-seq and have plenty of questions. Please be patient if my questions are too stupid. Here's my first one:

When I run tophat2 (2.0.13) on my paired-end Illumina dataset, it reports after "Preparing reads" about 37 Mio kept reads, each left and right, only 20-40k discarded. So far, so good. I understand that this is the Bowtie2 output. Once the run is completed, the "align_summary.txt" is reporting only 2.3 Mio reads each (Input). If it was mapped reads, I'd kind of understand, but input reads? What happened to >90% of the reads?

Since I am in a process of learning-by-doing, I would like to understand what I see here.

Thanks a lot!
abisko00

Last edited by abisko00; 08-06-2015 at 03:55 AM.
abisko00 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 07:25 AM.


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