SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat/Bowtie - number of reads aligned mgibson Bioinformatics 7 10-22-2011 08:04 PM
unique mapped reads from Mapsplice yuhj RNA Sequencing 1 09-25-2011 04:40 PM
prep_reads file in Tophat run shows a different number of reads gen2prot Bioinformatics 7 03-24-2011 01:50 AM
Regarding Unique reads, Unique alignments sridharacharya RNA Sequencing 2 09-20-2010 05:39 AM
unique reads for downstream analysis bioinfosm Bioinformatics 3 07-07-2009 01:30 PM

Reply
 
Thread Tools
Old 08-29-2011, 05:22 AM   #1
reut
Member
 
Location: Israel

Join Date: Oct 2010
Posts: 19
Default Different number of unique reads using TopHat -g

Hi,
I am running TopHat (v1.1.4) on single end reads (72bp)
I run TopHat several times, each changing only the '-g/--max-multihits' option: default (40), 2, 1
[I also use the --butterfly-search option in all cases]

After each run, I count the number of uniquely mapped reads in the output accepted_hits.bam by counting read ids that appear only once in the file.
I expect to get the same number of unique maps in each run, since it's the same data, however, I get a different number for each run. for example:
(-g 1): 23,177,858
(-g 2): 26,223,890
(-g 40): 29,025,648

Any idea why this happens?
Thanks!
reut 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 11:46 AM.


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