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hi,
i have small RNA seq data from ~ 50 isolated tumor cell samples (~700 mio reads) and found at least 1282 new miRNAs (predicted by two independent methods and supported by at least 100 reads) and thousands (>150 k !!!) of nc transcripts (no annotation known) also supported by >100 reads.
short outline of the analysis so far:
filter quality, remove adaptor, keep complete small RNAs between 13-37 nt
predict new miRNAs with mirDeep_star and nc transcripts with NorahDesk.
consolidate new miRNAs (from mirDeep_star) and use mirBase v20, gencode 19 annotation and a few other annotations (e.g. piwiRNAs) and the new found miRNAs to annotate the NorahDesk nc transcripts. but most of them left un-annotated.
finally, i mapped all 13-37 nt reads to these nc transcripts (stringent) and summed the reads for each sample and nc-transcript.
I wanted to ask you what kind of annotation could be done with these nc transcripts. is there a good method to estimate e.g. conservation among vertebrates (which degree? familiy, class, phylum, ... would be useful).
what else could be done - the small RNA transcriptome seems to be very complex?
best,
dietmar
i have small RNA seq data from ~ 50 isolated tumor cell samples (~700 mio reads) and found at least 1282 new miRNAs (predicted by two independent methods and supported by at least 100 reads) and thousands (>150 k !!!) of nc transcripts (no annotation known) also supported by >100 reads.
short outline of the analysis so far:
filter quality, remove adaptor, keep complete small RNAs between 13-37 nt
predict new miRNAs with mirDeep_star and nc transcripts with NorahDesk.
consolidate new miRNAs (from mirDeep_star) and use mirBase v20, gencode 19 annotation and a few other annotations (e.g. piwiRNAs) and the new found miRNAs to annotate the NorahDesk nc transcripts. but most of them left un-annotated.
finally, i mapped all 13-37 nt reads to these nc transcripts (stringent) and summed the reads for each sample and nc-transcript.
I wanted to ask you what kind of annotation could be done with these nc transcripts. is there a good method to estimate e.g. conservation among vertebrates (which degree? familiy, class, phylum, ... would be useful).
what else could be done - the small RNA transcriptome seems to be very complex?
best,
dietmar