SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Secondary size selection for single cell RNAseq on NextSeq 500 help sallen Illumina/Solexa 0 03-08-2016 11:21 AM
any tools to test if my RNAseq data is enough? mihuzx RNA Sequencing 8 04-14-2014 06:00 AM
get RNASeq data for cell types and cell lines Fernas Bioinformatics 2 12-22-2013 08:52 AM
Single cell RNAseq _ Transcriptome sequence honey Bioinformatics 5 08-21-2012 09:43 AM
RNAseq from single cell RT? pie Sample Prep / Library Generation 0 10-29-2010 08:41 AM

Reply
 
Thread Tools
Old 11-16-2016, 08:19 AM   #1
jspagnuo
Junior Member
 
Location: Switzerland

Join Date: Sep 2012
Posts: 2
Default differences between alignment tools for single cell RNAseq data

I was wondering whether there were any major differences in the readout from single-cell RNAseq reads aligned with traditional short-read alignment tools like Bowtie2 vs a pseudoaligner like Kallisto.

I wanted to leverage the speed of pseudoalignment and use the transcript-compatability counts (TCC) to decrease the alignment bottleneck when dealing with 50,000 cell libraries.

I was told earlier today that Kallisto and clustering on a TCC matrix would produce spurious results, however I'm not convinced given the results in the Ntranos, 2016 paper in Genome Biology.

Last edited by jspagnuo; 11-17-2016 at 12:01 AM.
jspagnuo is offline   Reply With Quote
Reply

Tags
alignment, clustering, rna-seq, single cell

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 09:38 PM.


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