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Old 07-09-2019, 07:31 AM   #232
bartn
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Location: Europe

Join Date: Jul 2019
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Quote:
Originally Posted by GenoMax View Post
Since you asked for 30K reads you got 30K paired-end reads.

I would sugegst trying without the metagenome=t option for a single small input fasta. If you do have the entire genome then use that in your randomread generation step along with the plasmid.
Yes, that does seem to increase the mapping percentages. Any idea why it is not working with meta option? Changes read length and insert size does not seem to do much..
The plasmid is about 0.5MB with 562 transcripts. Median transcript size is 830bp, so that could be a bit short, (but then I would expect the same with the meta option off)

I will also look for another suitable (small) genome. I don't want to add the complete genome because it should finish quick, since it's for testing purposes of tools and pipelines.

(btw, one other small thing. Adding any statistic file in the arguments will give the small summary in the stdout (like I posted before). Otherwise it will not be printed. Not sure if that is expected behavior)
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