Celia,
From my understanding your N50 for transcriptome assembly should be pretty low. You're just not going to have large contigs when the average spliced gene is something like 1500-2000 base pairs. Then, depending on your RNA extraction and purification methods, you might have also captured microRNAs. To a certain extent you probably have some genomic contamination, and certainly a lot of pre-spliced mRNAs. Then, what's your coverage on lowly expressed genes? For larger, but lowly expressed genes, you probably have a bunch of small contigs. Anyway, I wouldn't worry about the N50 for transcriptome assembly so much. I'd much rather see what the size of the 5,000th and 10,000th contig is to get a measure of how "complete" the transcriptome is. And unless you have the whole body of the animal and a variety of ages (including embryonic), I wouldn't expect you to get much more than 10K reasonably well assembled genes, if that.
I can't really help with the other question though, I'm still behind on the actually "doing" of the analysis, but do you mind sharing what kind of specs the computer you where running ABYSS on had for processors/RAM?
From my understanding your N50 for transcriptome assembly should be pretty low. You're just not going to have large contigs when the average spliced gene is something like 1500-2000 base pairs. Then, depending on your RNA extraction and purification methods, you might have also captured microRNAs. To a certain extent you probably have some genomic contamination, and certainly a lot of pre-spliced mRNAs. Then, what's your coverage on lowly expressed genes? For larger, but lowly expressed genes, you probably have a bunch of small contigs. Anyway, I wouldn't worry about the N50 for transcriptome assembly so much. I'd much rather see what the size of the 5,000th and 10,000th contig is to get a measure of how "complete" the transcriptome is. And unless you have the whole body of the animal and a variety of ages (including embryonic), I wouldn't expect you to get much more than 10K reasonably well assembled genes, if that.
I can't really help with the other question though, I'm still behind on the actually "doing" of the analysis, but do you mind sharing what kind of specs the computer you where running ABYSS on had for processors/RAM?
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