SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
STAR: ultrafast universal RNA-seq aligner alexdobin Bioinformatics 218 04-02-2018 06:59 PM
STAR rna seq Aligner installation arcolombo698 Bioinformatics 10 10-25-2016 10:31 AM
different read lengths in rna-star frymor Bioinformatics 0 08-17-2015 12:07 AM
2nd Pass Alignment with STAR for RNA-sequencing cbaudo RNA Sequencing 3 03-04-2015 04:59 AM
merging a tab and a fasta file arg General 2 10-21-2010 11:53 AM

Reply
 
Thread Tools
Old 09-16-2015, 09:02 AM   #1
ebe
Junior Member
 
Location: France

Join Date: Apr 2013
Posts: 6
Default RNA-Star : SJ.out.tab differents according to 'outFilterType' value?? and

Hello,

we are using RNA-Star to our project (thank to authors!).
I don't understand a difference observed about the SJ.out.tab files (file with junctions) according to the value of 'outFilterType' option (Normal or BySJout).

Indeed, Alexander Dobin wrote (https://groups.google.com/forum/#!ms...w/VmgoGKSE9qQJ) :
"However, if you use --outFilterType BySJout option, splicing of alignments in the Aligned.out.sam will only be allowed across the junctions which pass the filtering into SJ.out.tab.
This option makes Aligment.out.sam file consistent with SJ.out.tab file."

So I had understood that the SJ.out.tab files should be the same, but not the sam files (file with alignments, from which the SJ.out.tab is created).
But I have two different SJ.out.tab files (all options except outFilterType are identical).
Could anyone explain to me why?
The other options are:
--outSJfilterReads unique --outSJfilterOverhangMin 29 12 12 12 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterIntronMotifs None --alignSJoverhangMin 5

Thanks!
ebe is offline   Reply With Quote
Old 09-18-2015, 07:40 AM   #2
ebe
Junior Member
 
Location: France

Join Date: Apr 2013
Posts: 6
Default

The response from Alex Dobin, STAR's author :
using the --outFilterType Normal vs BySJout options will create slightly different SJ.out.tab counts for the following reason.
Imagine that you have a read two junctions, with only 1st junction passing the filter.
Then with the Normal option, the 1st junction will be counted in the SJ.out.tab.
If the BySJout option is used, the entire read alignment may be prohibited because of the 2nd junction, and then the 1st junction will be not counted in the SJ.out.tab.

An even more complicates situation may arise if after prohibiting the 3nd junction, the read maps into a different locus with a junction different from the 1st.

closed thread...
ebe is offline   Reply With Quote
Reply

Tags
sj.out.tab, star

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 11:13 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO