Hi, Just to clarify. In STAR, if `--sjdbGTFfile` was used in the genome indexing step it is no longer necessary to use the flag `--sjdbGTFfile` …

Hi, Does anybody have experience performing eQTL analysis and/or somatic mutation analysis of bulk RNA-seq data (without normal sample)? What tool/s/pipeline did you use? Thanks …

Hi, I would like to use SoupX for ambient RNA removal. However, I am using barcode-gene matrix datasets downloaded from NCBI GEO which don't always …

Hi, I am working with a WGBS dataset and have done alignment and methylation calling with Bismark and DMR analysis with metilene. So far I …

Hi, Can PHLAT (HLA genotyping) be used with single cell RNA-seq (e.g. 10x platform)? Thanks and good day.

Hi, From what I understand, for smart-seq2 sequencing files there are multiple fastq files per sample with one single/pair per cell. However, in NCBI GEO …

Hello, I am trying to work with metagenome Illumina simulated reads to test a pipeline. The normal way to do that is to use simulator …

Hi! Does anyone know how common differentially methylated regions (DMRs) (or just methylated regions) are? Say, in a 10,000bp region how many DMRs can one …

Hi, I have 16 RRBS samples: 4 control-female, 4 control-male, 4 treatment female, 4 treatment-male. I wanna analyse for DMR using methylkit. I can easily …

<p>Are there any good DMR software available for running on data for DNA methylation data? Googling results in many different software, but I want to …