biozzq
biozzq
Dear all, Could permutation test be included in this software? It will be helpful when defining a thresold. Thank you very much. Best regards, Zheng zhuqing
Hi @all, Do you have any recommended software used for downstream analyzing Bismark outputs, such as detecting regions of differential methylation, calculating methylation rate for targeted region, creating average methylation...
Dear all， I have a basic question. In many published papers, I found that they usually describe the binary nature of scATAC data, also in your paper-(`A bin with value...
Dear all, I would say that salmon is so fast to report the TPM and read counts for each transcript or gene, and I always use salmon+tximport+edgeR to detect the...
Hi, Since my focus is on specific regions and variants on the genome, I'm wondering if I can remove non-targeted positions from the reference panel before imputation to reduce the...
Dear @brentp Recently, I tried to use smoove to detect CNV using the BAM file generated by BWA-MEM as input. However, lumpy_filter always gave me an error: "Segmentation fault (core...
Dear @stschiff The factor 2 will cause the inconsistencies when plotting effective population size. And this has been disscussed here https://github.com/stschiff/msmc2/issues/17#issuecomment-433145181. You should also update the Ne plot in the...
Dear @lczech, I have four pooling sequencing libraries. I have finished SNP calling using bwa+GATK and a total of 9.8 M SNPs (after filtering for depth and missing rate) have...
Dear all, Recently, I found that FAN-C ran slowly and have discussed here (https://github.com/vaquerizaslab/fanc/issues/42). I will try the pipeline recommended by @kaukrise . Does anyone have experience to prepare the...
Dear all According to your published paper, I defined regions with a z-normalized similarity score ≤−1.2 and a signal-to-noise ratio of r ≥ 0.6 as the significant changing. When using...