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Old 09-22-2016, 09:49 AM   #1
mavadhani
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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 genomespace.org (http://recipes.genomespace.org/view/6) that utilize tophat (v8.1) to align sequences on genepattern.broadinstitute.org. 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 (http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi). 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.
Madhavi
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Old 10-21-2016, 11:46 AM   #2
bhill
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Location: Cambridge, MA

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Default

Hello Madhavi,

Are you still in need of assistance with this issue?

Best

-Barbara
__________________
Barbara Hill
Software Test Engineer
Cancer Informatics Development
Broad Institute of Harvard and MIT
Cambridge, MA
USA
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