Hi,
I am interested in identifying 5' UTR and 3' UTR of known mouse genes linked to olfaction. I have access to the CDS, poor annotations of the 5' and 3' from Biomart, CAGE data for the promoters and lots of RNASeq data (10 samples with 30-80M reads, paired-end but unstranded) from the litterature.
I have read (Widespread and extensive lengthening of 3' UTRs in the mammalian brain Miura 2013) that in the CNS there are longer 3' isoforms, often tied to local transport and translation in dendrites or axons.
Do you know what type of tissue is used for 'official' annotations (mm10 for example) done with RNA Seq data? In IGV I see very different types of 3' UTR in the olfactory epithelium, but this could be a tissue specific thing.
What would you use for annotating 3'UTR?
I am thinking of trying out IsoSCM (Jan2015, Shenker), but is very recent. I have also heard some good about TrinityRNASeq. Cufflinks is rather bad for this task, it missed isoforms I could see on IGV (and then confirmed with Northern Blots).
Thanks a lot for your help.
Cyril
I am interested in identifying 5' UTR and 3' UTR of known mouse genes linked to olfaction. I have access to the CDS, poor annotations of the 5' and 3' from Biomart, CAGE data for the promoters and lots of RNASeq data (10 samples with 30-80M reads, paired-end but unstranded) from the litterature.
I have read (Widespread and extensive lengthening of 3' UTRs in the mammalian brain Miura 2013) that in the CNS there are longer 3' isoforms, often tied to local transport and translation in dendrites or axons.
Do you know what type of tissue is used for 'official' annotations (mm10 for example) done with RNA Seq data? In IGV I see very different types of 3' UTR in the olfactory epithelium, but this could be a tissue specific thing.
What would you use for annotating 3'UTR?
I am thinking of trying out IsoSCM (Jan2015, Shenker), but is very recent. I have also heard some good about TrinityRNASeq. Cufflinks is rather bad for this task, it missed isoforms I could see on IGV (and then confirmed with Northern Blots).
Thanks a lot for your help.
Cyril
Comment