Genomic UTR sequencing alignment and quality control

YL Yiting Lim
SA Sonali Arora
SS Samantha L. Schuster
LC Lukas Corey
MF Matthew Fitzgibbon
CW Cynthia L. Wladyka
XW Xiaoying Wu
IC Ilsa M. Coleman
JD Jeffrey J. Delrow
EC Eva Corey
LT Lawrence D. True
PN Peter S. Nelson
GH Gavin Ha
AH Andrew C. Hsieh
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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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