Raw sequencing reads produced by Illumina’s bcl2fastq 1.8.4 software were processed to exclude read pairs failing default (PF filtering) quality checks. FastQC (v0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to evaluate raw sequencing reads. All reads were aligned to hg19 using Bowtie (v1.0.0)48, only reads aligning to standard chromosomes (chr1:22, X, Y, M) were retained for further analysis. The reads with low quality were filtered and duplicates were marked using Picard (v2.21.6). 5′-UTR and CDS coverage was calculated using GATK “DepthOfCoverage” (https://gatk.broadinstitute.org/hc/en-us/articles/360041851491-DepthOfCoverage). ContEst (v3.6)49 was used to estimate the level of cross-individual contamination in matched normal-tumor pairs from all mCRPC patients and PDX samples that were sequenced.
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