Hi everyone,
This is my first time trying to analyse RNAseq data. I've got the results from a paired end read experiment, where fragments were selected at 240bp for 75bp reads, so there's probably some overlap and i'm not sure the wiggle track can be trusted.
I've attatched a pic of one of my odd results, i'm not sure whether it is down to me badly selecting parameters, or whether there are issues when there are small spaces between transcribed genes? The EMBL track is automated annotations, and I didn't use them to guide tophat as we "know" a lot of them are wrong, but 01890 and 01880 are definitely seperate genes, based on experimental results (i'm also new to gbrowse, and haven't got it configured correctly so it seems to think all the exons are separate genes...but that doesn't matter right now!). CUFF .3178 including the well transcribed region and the rather flat bit next to it also doesn't seem intuitive.
Any tips?
Thanks.
This is my first time trying to analyse RNAseq data. I've got the results from a paired end read experiment, where fragments were selected at 240bp for 75bp reads, so there's probably some overlap and i'm not sure the wiggle track can be trusted.
I've attatched a pic of one of my odd results, i'm not sure whether it is down to me badly selecting parameters, or whether there are issues when there are small spaces between transcribed genes? The EMBL track is automated annotations, and I didn't use them to guide tophat as we "know" a lot of them are wrong, but 01890 and 01880 are definitely seperate genes, based on experimental results (i'm also new to gbrowse, and haven't got it configured correctly so it seems to think all the exons are separate genes...but that doesn't matter right now!). CUFF .3178 including the well transcribed region and the rather flat bit next to it also doesn't seem intuitive.
Any tips?
Thanks.
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