[yueluo]

You need the newest version of tophat

http://ccb.jhu.edu/software/tophat/index.shtml

TopHat 2.0.12 release 6/24/2014
Version 2.0.12 is a maintenance release with the following simple fix:
This version is compatible with Bowtie2 v2.2.3.

[GenoMax]

I got this error:

[2014-07-04 10:52:25] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-07-04 10:52:25] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: TopHat requires Bowtie 0.12.9 or later

It seems to me there is a problem with the version of bowtie I have installed, perhaps to old? If you could please give some clue about how to solve this problem?
Thanks in advanced

If you only have bowtie (v.1.x) installed then you may need to add the following option

$ tophat --bowtie1 -r 20 test_ref reads_1.fq reads_2.fq

It may be better to install bowtie2 (http://sourceforge.net/projects/bowt...les/bowtie2/)?

Or it may be a simple fix of adjusting your $PATH so bowtie directories are included there.

[lamaga]

Error in testing the installation of Tophat

I'm a brand new person in RNA-Seq and a beginner in bioinformatics as well. So my apologies if my question is naïve or it has been posted already. Recently I installed Tophat v2.0.12, with Bowtie, SAMtools and Boost libraries, in Ubuntu 12.04 lts 32-bits. However when I tried to test the installation

tophat -r 20 test_ref reads_1.fq reads_2.fq


I got this error:



[2014-07-04 10:52:25] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-07-04 10:52:25] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: TopHat requires Bowtie 0.12.9 or later

It seems to me there is a problem with the version of bowtie I have installed, perhaps to old? If you could please give some clue about how to solve this problem?
Thanks in advanced

[GenoMax]

I was using Bowtie 2.2.1. Won't upgrade to 2.2.3.

[ErikFas]

Downgrading to Bowtie 2.2.2 did the trick! Must have been a bug or something in 2.2.3...

[ErikFas]

Damn =P I'll do that and see if it works. Thanks for all your help, regardless!

[GenoMax]

I am stumped.

Give a real sample a try to see if that works.

[ErikFas]

No, I have a plain bowtie2-build as well.

[GenoMax]

But no plain bowtie2-build (the -l is for 64-bit indexes but they are not supported by TopHat as yet)?

[ErikFas]

Yeah, a bunch of them (bowtie2-build-l/s/l-debug/s-debug).

[GenoMax]

Definitely.

If you do not have the bowtie-build.log then that means the indexes are missing. Do you have bowtie2-build in your path?

[ErikFas]

Nope, only got the four we've already been through... So, something related to that, mayhap?

[GenoMax]

True. Not sure what to say next.

Do you also have all these other bowtie related log files?

bowtie_build.log
bowtie.left_kept_reads.log
bowtie.left_kept_reads_seg1.log
bowtie.left_kept_reads_seg2.log
bowtie.left_kept_reads_seg3.log
bowtie.right_kept_reads.log
bowtie.right_kept_reads_seg1.log
bowtie.right_kept_reads_seg2.log
bowtie.right_kept_reads_seg3.log

[ErikFas]

bowtie.left_kept_reads.log:

100 reads; of these:
  100 (100.00%) were unpaired; of these:
    59 (59.00%) aligned 0 times
    41 (41.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
41.00% overall alignment rate

prep_reads.log:

prep_reads v2.0.11 (4203)
---------------------------
0 out of 100 reads have been filtered out
0 out of 100 read mates have been filtered out

Looks error-free to me.

[GenoMax]

Let us look at some more log files. Can you check prep_reads.log, bowtie.*.log to see if there are any errors there?