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Old 09-22-2016, 09:49 AM   #1
Junior Member
Location: baltimore

Join Date: Jul 2016
Posts: 9
Default Help with TOPHAT on genepattern

Hello everyone!

I am new to bioinformatics. With a strong background in molecular biology and biochemistry, I am looking to transition to bioinformatics.

I want to look at differential gene expression in a set of RNA-seq data. I am using the recipes from ( that utilize tophat (v8.1) to align sequences on Here is what I did-

1. Downloaded the fasta(.fna) file with the genome sequence and built an index using bowtie2 downloaded on my computer. Indexing was not a problem. It worked just fine. I also downloaded the .fasta format and indexed the file using bowtie2. Neither formats appeared to have any difference.

2. Downloaded the gff file from NCBI for my bacterium. When I unzip and open this file in notepad, I dont see it the neatly tabulated file you would expect to see in a gff! I also downloaded the file in genbank format and converted it into gff2 using this online tool ( I copied the output into notepad and saved it with a .gff extension. The former version is giving me an error (Unable to detect the name of the bowtie index) while the latter version gives me a null.accepted.hits. With this, I run into problems in the next step while using cufflinks. I dont know what to do.

Any help/suggestions welcome.

Thanks in advance.
mavadhani is offline   Reply With Quote
Old 10-21-2016, 11:46 AM   #2
Junior Member
Location: Cambridge, MA

Join Date: Aug 2011
Posts: 5

Hello Madhavi,

Are you still in need of assistance with this issue?


Barbara Hill
Software Test Engineer
Cancer Informatics Development
Broad Institute of Harvard and MIT
Cambridge, MA
bhill is offline   Reply With Quote

genepattern, rna-seq advice, tophat

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