NOVOPlasty
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ndierckx
help for detecting heteroplasmy
Hi everybody, I'm Eda. Recently, I am going to detect the heteroplasmy within chloroplast genome to investigate wether there is biparental heteroplasmy within my samples. I am really glad to find the NOVOPlasty since it can detect heteroplasmy for chloroplast genome. However, there is no detailed introductions to this analysis and I always obtained blank result files for heteroplasmy analyses. Could anybody help me for the settings of the configure file??? Thanks a lot!
I have already obtained the complete chloroplast genomes assembled by my colleague, and took them as their own reference genome and seed genome, while the results files also were blank.
Hi, could you send me the log, so I can check if all the parameters are correct. And do you have enough coverage for heteroplasmy detection? I haven't test it much on chloroplast genome but it is more complicated because of the many duplicated regions in the mitochondrial genome
The mean coverage of cp genomes ranged from 200 to 7900 X. So, I think the coverage of cp genomes is enough to detece heteroplasmy. I have deleted the log file. I will conduct this analysis this afternoon and upload the log files here. Thanks a lot
Reading Input......OK
Scan reference sequence......OK
Building Hash Table......OK
Subsampled fraction: 100.00 %
Retrieve Seed...
However, there was no futher infomation for the next step. I guess there may be some errors in my configure files.
Your MAF is way too low, you are looking for heteroplasmy of 0,01%, that is impossible. If you want 1%, put 0,01. I will put an automatic allert in the next version. Try what it gives with 0,01. But i see you have reads of 90bp, that means they are old i guess, so less accurate. So definitely don't go below 0.01
Thanks. Actually, I used 0.01 for MAF first. The result files were still blank.
ok, and when you did it before, it also got stuck at Seed retrieval? With a MAF lower than 0.01 that can happen
Exactly, I have arond 50 accessions that need to conduct the heteroplasmy detection.
ok. The serve maintaince will be finished tommorrow. After that, I will upload my seed file.
results.zip hi, I have analyzed another sample with two different MAF. I obtained the results of heteroplasmy. Here are the all results.
I don't know whether the analysis is correct. In addition, the results confused me.
Did you use the chloroplast assembly as a reference and seed or some online reference?
Because you have a lot of homoplasmies, so your reference is probably not from that dataset? if you run again, please use the extended log (set to 1), then I can see when something went wrong. And you should try a high coverage dataset first
Ah sorry coverage seems enough.., but results are bit weird indeed, if you send me one dataset, I can also try myself if you want
But since all heteroplasmy is found in one short region, I would guess there is no heteroplasmy, something surely went wrong in that area
yes, I used the assembled chloroplast genome as reference genome. I am sure the chloroplast genome is consistent with the reads I used. I wonder whether I should use the raw reads from the whole-genome resequencing or use the filtered data that only contained chloroplast reads??
hello, the reads should be the raw whole-genome sequences or the filter data that only contained chloroplast reads??
We used the complete cp genomes of related species as reference genomes to screen out the cp genomes reads. The raw reads are ～40 G