CHM13 RNA-seq Bowtie2 alignments to CHM13v2.0 (minus chrY) and unique genome-wide 21mer filtering (unstranded)
Poly-A+ RNA-seq was performed on CHM13 in duplicate (A and B) and sequenced with 150-bp paired-ended reads. Reads were adapter trimmed, quality filtered (-q 20), and length filtered (-m 100) with Cutadapt (v2.7). Reads were then mapped with either Bowtie2 (v126.96.36.199) default or -k 100 (allowing up to 100 multi-mappers) and then filtered with samtools view F1548. Unique genome-wide 21mers were generated through Meryl (https://github.com/marbl/meryl).
The reads mapped with -k 100 were filtered with these unique genome-wide 21mers through one of two methods: