Is there any method to run tophat ?

Question

[Chan]

im very frustrated

im novice to Bioinformatics and RNAseq

i started to use tophat as my first tool for allignment

i want to run 2 or more

ex. 1_control_1.fastq,1_control_2.fastq, 1_condition_1.fastq,1_condition_2.fastq , 2_condition_1.fastq, 2_condition_2.fastq

any way to run them together in one terminal?

if you know way to run by python scripts (ex. s or other, plz let me know scripts...

[finswimmer]

Hello bku0331,

You should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[ATpoint]

Hi bku0331, welcome to Biostars.

I recommend to start reading this workflow. Also I agree with finswimmer that tophat is deprecated. Modern alternatives are STAR or HISAT2 if you want to do alignments, or tools like salmon or kallisto for estimation of transcript abundances. If you need details, please use the search function here, together with google to find some of the numerous questions, blogs and tutorials on RNA-seq. Spend some quality time on reading them to get a proper background, and come back here in case you get stuck.

[igor]

Additionally, you may find this post helpful: https://gencore.bio.nyu.edu/salmon-kallisto-rapid-transcript-quantification-for-rna-seq-data/

[mbk0asis]

Check out this thread to run mutiple files using an alignment tool, and switch to 'Hisat2' or something else as people are saying!