https://divingintogeneticsandgenomics.com/tags/wes/ Recent content in WES on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Wed, 22 Nov 2017 12:35:00 -0800 https://divingintogeneticsandgenomics.com/archive/run-gistic2-with-sequenza-segmentation-output-from-whole-exome-sequencing/ Wed, 22 Nov 2017 12:35:00 -0800 https://divingintogeneticsandgenomics.com/archive/run-gistic2-with-sequenza-segmentation-output-from-whole-exome-sequencing/ Convert sequenza output to gistic input Gistic was designed for SNP6 array data. I saw many papers use it for whole exome sequencing data as well. I have the segment files from sequenza and want to convert them to the gistic input. Input format for gistic: segment file: (1) Sample (sample name) (2) Chromosome (chromosome number) (3) Start Position (segment start position, in bases) (4) End Position (segment end position, in bases) https://divingintogeneticsandgenomics.com/archive/bwa-mem-multi-mapping-reads/ Thu, 10 Aug 2017 11:27:00 -0700 https://divingintogeneticsandgenomics.com/archive/bwa-mem-multi-mapping-reads/ An error I was using TEQC to do quality control of my WES bam files aligned by bwa-mem. My data are paired end, so a function reads2pairs is called to make the paired-end reads to be a single fragment. I then get this error: > readpairs <- reads2pairs(reads) Error in reads2pairs(reads) : read pair IDs do not seem to be unique I asked in the bioconductor support site and went to the source code of that function.