<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks Carson for the response. I understand that est2genome=1 does not use any ab initio gene predictions, but simply identifies ests based on alignment. I'm a little confused because I ran maker on my assembly before, using the same parameters ( including est2genome=1). I got a very good result with > 20,000 transcripts and proteins. <div><br></div><div>Then I was able to get an improved assembly, where many scaffolds were combined into superscaffolds. So I reran maker on this assembly. Same parameters, same transcriptome and proteins files. Now, I see such drastically different results: Only 500+ genes and transcripts. My scaffolds are now bigger than before, so I'm not sure how this is happening. These were the results I sent you.</div><div><br></div><div>Another odd thing I noticed (and I am hesitant to report this because perhaps it is due to some sort of error on my part): I ran maker on the improved assembly the first time and maker did not complete in the 48 hours I allocated. But I had 19,000+ transcripts in the unfinished output. When I reran maker, just changing the time allocated, it completed much faster, but is giving much fewer transcripts and proteins as output. Could something like this happen? If not, then I'm guessing I must have changed something although I'm pretty sure that I did not change anything other than the time allocated. I've attached the trascripts and proteins files from the first time I ran maker on my improved assembly.</div><div><br></div><div>Thanks again for your help</div><div>Dhivya</div><div><br></div><div></div></body></html>