Hallo everyone,
I'm new in the forum. Recently I've been dealing with some NGS data coming from the Illumina platform. I used the classical Tophat-Cufflinks pipeline to analyze the data.
But I'm dealing with the issue of visualizing RPKM values in a genome browser.
UCSC does not support GTF files, nor GFF, I can upload the wig files, but that would help only with the raw reads.
In another thread on this forum someone suggested a modification of the GTF file that would fit in Gbrowse. I tried to do that and uploaded the result on Gbrowse in MGI. No output. the track is just not visualized (even if no error output is given).
In this very moment I'm somehow stuck there, can anyone help me with that?
D.
I'm new in the forum. Recently I've been dealing with some NGS data coming from the Illumina platform. I used the classical Tophat-Cufflinks pipeline to analyze the data.
But I'm dealing with the issue of visualizing RPKM values in a genome browser.
UCSC does not support GTF files, nor GFF, I can upload the wig files, but that would help only with the raw reads.
In another thread on this forum someone suggested a modification of the GTF file that would fit in Gbrowse. I tried to do that and uploaded the result on Gbrowse in MGI. No output. the track is just not visualized (even if no error output is given).
In this very moment I'm somehow stuck there, can anyone help me with that?
D.
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