SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat2 errors ahmetz Bioinformatics 25 09-04-2013 06:24 AM
tophat2 problem: No such file: left_kept_reads.m2g_um.candidates_and_unspl.bam tgenahmet Bioinformatics 2 05-24-2012 01:42 PM
tophat2 installion problem IceWater Bioinformatics 1 05-09-2012 12:09 AM
Ion torrent for insertion/deletion arrayprofile Ion Torrent 4 09-28-2011 03:11 AM

Reply
 
Thread Tools
Old 04-23-2012, 12:29 AM   #1
Bukowski
Senior Member
 
Location: UK

Join Date: Jan 2010
Posts: 390
Default TopHat2 insertion bed outputs

Unlike other people here I don't seem to have any problems actually running TopHat2 and the actually mapping results look pretty similar to the previous version of TopHat we were running.

However it is reporting a lot more events in the insertions/deletions bed file. I will admit upfront that I'm using a home-built Bowtie index between the two rather than the iGenomes ones, but I don't understand why that would be responsible for this kind of output in the insertions.bed:


1 567684 567684 A 13
1 567684 567684 AT 10
1 567684 567684 GTG 12
1 567684 567684 AATC 2
1 567684 567684 GATCG 8
1 567684 567684 GATCGG 2
1 567684 567684 CCTTACTACC 1
1 567684 567684 CCTTACTACCAG 1
1 567685 567685 T 1
1 567685 567685 TG 12
1 567685 567685 AGATG 1
1 567685 567685 TATGATAGTGA 6
1 567685 567685 TGAATATGATAGTGA 4
1 567686 567686 G 2
1 567686 567686 TC 2
1 567686 567686 GAG 1
1 567686 567686 TCAA 3
1 567686 567686 GATGA 2
1 567686 567686 ACCACACCTC 1
1 567687 567687 CAGA 2
1 567688 567688 A 3
1 567688 567688 GGTGAAACC 1
1 567688 567688 TAGATCGGAAGAG 1
1 567689 567689 AAA 1
1 567689 567689 CCCGC 1
1 567689 567689 ATACTG 1
1 567689 567689 GGAAGAG 3
1 567689 567689 GGAAGAGCGT 1
1 567690 567690 A 4
1 567690 567690 TAG 1
1 567690 567690 ATCAAACACA 1


And this situations is repeated throughout the file to the tune of about 4 million entries.

Any insight appreciated..
Bukowski is offline   Reply With Quote
Reply

Tags
bed, insertions, tophat, tophat2

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 02:14 PM.


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