Hello guys, I did run freebayes and performed some filtration on the output. - removing indels, and discardmulti-allelic sites. There were long-looking SNP sequences with …

ATAC-seq reads pile-up showing allelic bias at SNP sites rs12895055 and another linked SNP rs11624408 ![enter image description here][1] [1]: https://iili.io/Fz6Lu4.png

I am using [GATK somatic-CNV pipeline][1] for some hg38 human sample (normal-tumor matched). In CollectAllelicCounts interval_list ([here][2] and [here][3] the discussions) I have tried to …

I wish to compare two biological conditions with respect to their open chromatin. I use ATAC-seq as my assay. My strategy has thus far been …

Hi, To check for ASE, I performed multisample gDNA variant calling using GATK and got heterozygous biallelic sites for which I looked for RNA-seq read …

The following fastqc report is common to most replicates of a mRNA-seq experiment: there's bias in the beginning of the reads in the '[Per base …

Hi Everyone, I performed targeted RNA-sequencing, in which we used a probe pool originally designed for exome capture to capture a transcript of interest in …

I'm looking at the encode ATAC-seq data analysis pipeline (https://www.encodeproject.org/pipelines/ENCPL035XIO/) and they recommend you trim the reads to 30bp. I'm having trouble understanding the reasoning …

I can get the allelic depth of any SNP by using pile-up. However, I need to get the coverage of gene in the exome sequence …

I have more than 500 samples (or thier bam files). I also have more than 1000 snps in snp table as shown below. I need …