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Old 10-05-2016, 09:24 AM   #1
mavadhani
Junior Member
 
Location: baltimore

Join Date: Jul 2016
Posts: 9
Default Help with genes.gct file on IGV

Hello All!

I am using RNAseq data from a bacterium to identify genes that show differential expression. I used the genepattern platform to align my reads in the fastq files to the genome using TOPHAT that generated the .bam files, and then to subsequently identify RNAseq reads that show differential expression I used Cuffdiff module. This generated the genes.gct file. I am able to load the .fasta format of the genome and the sorted bam files of the samples I want to analyze on IGV without a problem. However, I am having trouble loading my genes.gct file on IGV. I am getting the following error-


"The probes in the file
https://dm.genomespace.org/datamanag...hani/genes.gct
could not be mapped to genomic positions. This can be corrected by specify a probe mappingfile from the Preferences window (Probes tab), or by specifing the genomic positions in the expression data file. Please see the user guide for more details."

I tried changing the expression probe mapping options under the probes tab of preferences menu. But that does not seem to help.

Another thing I have to mention is the the genes.gct file has 4 columns with the first one being the tracking id, the second column with the description which contains the genome id and the cds but no annotation. The third and the fourth columns appear to contain levels of different RNAs in my 2 samples.

I apologize for the lengthy message, but I hope you will understand that I am now to this and anxious to get things moving.

Any suggestions/help would be much appreciated.

Thanks,
Madhavi
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differential expression, genepattern, genes.gct, igv, rnaseq

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