chrishah
Result contig with many "N"
Dear Christoph,
I used mitobim for a 5G Illumina 2*100 library, with a 13K reference. The command is as following, "mitobim -end 30 --quick ref.fasta --clean -sample X1 -ref XX -readpool all.fastq" After iteration19, the run finished with many "N" (> 50% length) in the final contig. I am wondering if it is a normal output? Can I fill these "N" by any method?
Best regards, Runsheng
Hello,
No, it's not normal. Ideally all gaps should have been closed. Usually if you end up with lots of N's your coverage is borderline low and you simply have no reads to cover the gaps.
In your case it sounds like you have plenty of data though. Depends a bit on the library/organism though. Is this a genomic library, i.e. containing both nuclear and mt reads? In genomic libraries, mt coverage usually is substantially higher than nuclear coverage, and you should get full mt coverage even if the nuclear data is very fragmented and unsuitable for assembly, but everything is possible.
Could you just quickly check the coverage in the regions that are not N's. If your coverage is high there than the issue is something else.
Or was the libary built from long range PCR products? I've seen cases of drastic differences of coverage between products, which resulted in fragmented assemblies.
I am happy to discuss your problem further but I need a bit more info about your data first.
cheers, Christoph
