Hi all!
I am studying differentiative alternative splicing in mouse brain. I am working with data from 3 different condition, 3 replicates each and an exon usage reconstruction with DEXSeq has already been done on these data. However I would like to reconstruct also the different isoforms and "translate" these information in terms of protein products. I read some papers about this topic and I am lost in the miriade of software available (and I'm blocked by the limitations of each of them). In particular I noticed IsoformEx, which provide very detailed information on the isoforms and the kind of differential splicing of differential promoter usage it provides, but I'm afraid that the data that I would obtain with this software wouldn't be consistent with those obtained with DEXSeq analysis. I know that Bioconductor provides a couple of software for isoform analysis, such as EBSeq and Bit Seq, but as far as I know, they don't do a nice analysis as the IsoformEx one. Would it be a right approach combining IsoformEx data with DEXSeq data or should I stick to the Bioconductor package to obtain more consistent results? Does anyone have experience with these software or other packages which would be good in my case (a tool which can reconstruct differential exon and isoform usage while keeping into account the biological variability of the different replicates)? Is IsoformEx a good choice for my analysis? Does exist a version which run on Windows, as I am not familiar with Linux which is required for IsoformEx.
The data are from both paired and single end sequencing which have been analyzed with the Tuxedo Suite of Bowtie, Tophat and Cufflinks. I know that the "natural pipeline" would be to identify the different isoforms with Cuffdiff but I read that this software has a lot of limitations, the results are very different with the different versions and they give much more false positives than DEXSeq, so I don't trust very much this tool.
I really hope you can help me, it's really frustrating not knowing where to start!
Thank you!
I am studying differentiative alternative splicing in mouse brain. I am working with data from 3 different condition, 3 replicates each and an exon usage reconstruction with DEXSeq has already been done on these data. However I would like to reconstruct also the different isoforms and "translate" these information in terms of protein products. I read some papers about this topic and I am lost in the miriade of software available (and I'm blocked by the limitations of each of them). In particular I noticed IsoformEx, which provide very detailed information on the isoforms and the kind of differential splicing of differential promoter usage it provides, but I'm afraid that the data that I would obtain with this software wouldn't be consistent with those obtained with DEXSeq analysis. I know that Bioconductor provides a couple of software for isoform analysis, such as EBSeq and Bit Seq, but as far as I know, they don't do a nice analysis as the IsoformEx one. Would it be a right approach combining IsoformEx data with DEXSeq data or should I stick to the Bioconductor package to obtain more consistent results? Does anyone have experience with these software or other packages which would be good in my case (a tool which can reconstruct differential exon and isoform usage while keeping into account the biological variability of the different replicates)? Is IsoformEx a good choice for my analysis? Does exist a version which run on Windows, as I am not familiar with Linux which is required for IsoformEx.
The data are from both paired and single end sequencing which have been analyzed with the Tuxedo Suite of Bowtie, Tophat and Cufflinks. I know that the "natural pipeline" would be to identify the different isoforms with Cuffdiff but I read that this software has a lot of limitations, the results are very different with the different versions and they give much more false positives than DEXSeq, so I don't trust very much this tool.
I really hope you can help me, it's really frustrating not knowing where to start!
Thank you!