TopHat with older versions of Bowtie

Question

[sarahmanderni]

Hi,

I wanted to ask if it is possible to run TopHat 2 with Bowtie 1. I need to mimic an already done experiment with this trend. But, running following code I got shown error:

module add samtools
module add bowtie/1.0.0
module add tophat/2.0.4
tophat -o output -p 12 -r 100 --mate-std-dev 110 --GTF hg19.gtf /hg19/Sequence/WholeGenomeFasta/genome X_1.fastq X_2.fastq

 Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

Answer 1

[Devon Ryan]

There's a --bowtie1 option that at least used to work.

[sarahmanderni]

Actually it still produces the same error. Is it very different if I use the combination of bowtie2 and tophat2 instead of combination of bowtie1 and tophat2?

[Devon Ryan]

Bowtie2 would generally produce a bit better alignments, at least if you have any indels. It also produces more meaningful MAPQ scores, though tophat2 removes them. Honestly, I wouldn't normally recommend that anyone use tophat to begin with, as it's painfully slow. But in your case, just download a previous version that matches what was used in the experiment that you need to mimic.