phyluce_assembly_assemblo_spades [contig length issue]

[kimchafer]

Hello, I am conducting research using myBaits UCE Coleoptera 1.1Kv1.

I followed the 'Phyluce Tutorial' exactly as described, and I am currently at the "Assemble the data" step, using 'phyluce_assembly_assemblo_spades' for the assembly.

However, I suspect that the length of the contigs produced by the analysis is abnormal. Here is the information:

Could you advise whether this result is plausible? If not, at which step is it likely that the problem occurred?

[brantfaircloth]

I think that these are values just after assembly? If so, those look pretty plausible. I'd go ahead and extract the UCE contigs from the entirety of contigs you assembled and re-evaluate the stats.

[kimchafer]

I am sorry for the late reply.

Following your recommendation, I continued the analysis and was able to recover more than 600 contigs during the 'Finding UCE loci' stage.

However, there is an oddity: the ratio of target loci contigs recovered to the total number of assembled contigs is very low (the highest is only 0.45%, and the lowest is 0.13%). Even the highest figure is significantly lower compared to the examples in the tutorial. Could this be normal, or might there have been an issue with the enrichment of target loci during the probe hybridization stage?

I would appreciate your opinion based on your experience. Thank you.

[brantfaircloth]

It's definitely possible - that ratio of UCE contigs to total contigs sounds extremely low. To me, it would suggest an enrichment issue.

[kimchafer]

Ok then this problem may stem from the molecular work step. I will take extra care during the next experiment especially in probe hybridization. I plan to sequence another test dataset soon and will share the results with you once that is completed at this issue.