Bcl2fastq cli tool

Paired-end reads were demultiplexed using Illumina’s bcl2fastq CLI tool. Fastqc was used to quality check the fastq files. Reads were then aligned using Bowtie2 (v2.2.5) with default parameters to the HG19 reference genome. MarkDuplicates from the genome analysis toolkit (GATK, v4.2.3) was used to mark duplicates. To remove low-quality/duplicate reads and sort the aligned BAM files, Samtools (v1.13) was used. Filtered BAM files were converted to BigWig files to view on the UCSC browser using bamCoverage (v3.5.1) from the Deeptools suite. MACS2 (v2.2.6) was used to compute and find enriched peaks in BAM files^{84 (link)}. To overlap peaks and remove problematic regions known to produce enriched signals in several next-generation sequencing experiments, known as blacklists (https://github.com/Boyle-Lab/Blacklist), bedtools intersect (v2.30.0) was used.

Single-end reads were demultiplexed using Illumina’s bcl2fastq CLI tool. Fastqc was used to quality check the fastq files. Reads were then aligned using STAR v2.7.3.a^{80 (link)} with default parameters to either the HG19 or MM10 reference genomes. To remove low-quality/duplicate reads and sort the aligned BAM files, Samtools (v1.13) was used. Filtered BAM files were converted to BigWig files to view on the UCSC browser using bamCoverage (v3.5.1) from the Deeptools suite. Cufflinks, Cuffquant, and Cuffnorm v2.2.1^{81 (link)} were used to assemble, quantify, and normalize transcripts (FPKM) to assemble the count tables, respectively.