Appropriate number of reads for assembling novel transcripts with Trinity?
I'd like to detect novel transcripts in a cancer sample with Trinity. I'm sequencing on an Illumina Hi-Seq (RiboZero capture, 150bp paired end reads). Are there any rules of thumb for how many reads I'll need to sequence to confidently assembly a majority of the transcripts?
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How would you know if you found the majority of novel transcripts if you don't know how many there are ? If you only found one novel transcript which was the cause of the cancer you are studying, isn't that also desirable ?