CHM13 RNA-seq Bowtie2 default alignments and Meryl unique k-mer filtering
The native RNA-seq libraries were done on CHM13 cells using oligodT during library prep and sequenced for 150bp paired-end reads.
Reads were adapter trimmed, quality filtered before mapped to chm13v1.1 with Bowtie2 default and then samtools F1548 filtered for paired-reads only
Mapped reads were then filtered through unique genome-wide 21 or 51mers
Megan Dennis (RNAseq library prep & sequencing)
Colin Shew (RNAseq library prep & sequencing)
Savannah Hoyt (mapping & filtering)
Rachel O'Neill
Arang Rhie (Meryl software for generation of unique kmers)