Simone Maestri
Simone Maestri
Hi Fritz, I am commenting here as I think the issue I am encountering is related to this one. I am merging SVs from 3 platforms, ignoring SV type and...
Dear Martin, I think this explains the issue I faced with these "difficult" samples, since outliers due to somatic mosaicism are not treated as such, and they participate in the...
Yes, I agree. Thank you for your quick answers. Simone
Dear @readmanchiu , I have a very similar issue. I am running Straglr and I am trying to count the number of "CAG" repeats in each read. In particular, I...
Hi, I just did a quick test with Straglr 1.4.1, specifying `--trf_args 2 7 7 80 10 50 500` parameter and using `CA*` as the motif in the `--loci` bed...
Dear @readmanchiu, actually I forgot to run minimap2 with `-Y` parameter, thank you for pointing this out. I was then able to run straglr exploiting the regex for specifying the...
Hi @readmanchiu , actually I realised every time a read has multiple alignments, all of them are reported in Straglr output file, while for my use case it would be...
Dear marghoob, I think I solved it filtering out from breakseq2_bplib_20150129_hg38.gff all chromosomes that are not in chr1-chr22, chrX, chrY, chrM. I was using file breakseq2_bplib_20150129_hg38.gff included in SVE, which...
Hi, I haven't worked with breakseq2 for a while. I don't remember if eventually I was able to run it using the docker container for [SVE](https://github.com/TheJacksonLaboratory/SVE). You may want to...
Ok, please let me know if you have any updates. Simone