Questions about the output file

[zshu-alt]

Hello, thank you very much for your software, the disease I study is a genetic disease, I want to find the Alu element in the SMN region, the SMN gene region is rich in Alu transposable elements, but the result file shows that no Alu has been detected on the SMN1 gene. Is it the filter condition? I would appreciate it if you could answer my questions.

[simoncchu]

Are you looking for germline/de novo pathogenic Alu insertions in the SMN1 gene? It may depends on the sample size I think. You can try with lower cutoff:

 The following cutoffs will be automatically set based on read depth (and also purity in the case of a tumor sample); 
 These parameters have been thoroughly tuned based on the use of benchmark data and also on a large cohort analysis. 
 For advanced users (optional major cutoffs):
 	--user: by default, this is turned off. If this option is set, then a user-specific cutoff will be used;
 	--nclip: minimum number of clipped reads;
 	--cr: minimum number of clipped reads whose mates map to repetitive regions;
 	--nd: minimum number of discordant pairs;

Also, there are different levels of output under the same folder as the vcf file. You may also check those ones.

[zshu-alt]

Thanks for your answer, I tried to lower the threshold to 1 and still did not find the Alu element in the SMN region. I even failed to find the relevant region in the original generated candidate_list_from_disc.txt or candidate_list_from_clip.txt file. Is it due to the homology of SMN1 and SMN2? You mentioned increasing the sample size, does it mean that I need to carry out case-control mode for detection? Or can multiple files be analyzed together?

[simoncchu]

Well, that's not what I could know. How do you know there must be Alu insertions within SMN? Here, I only try to help to resolve technic issues for using xTea, not for research questions.