CHM13 RNA-Seq Track Settings
 
CHM13 RNA-Seq (paired-end) unique genome-wide kmer filtering (unstranded)   (All mRNA and EST tracks)

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Data schema/format description and download
Assembly: Human Jan. 2022 (T2T CHM13v2.0/hs1)

Description

CHM13 RNA-seq Bowtie2 alignments to CHM13v2.0 (minus chrY) and unique genome-wide 21mer filtering (unstranded)

Methods

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 (v2.3.5.1) 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:

  1. Locus-specific unique genome-wide 21mer filtering (overlapSelect -overlapBases=21; UCSC tools (GenomeBrowser/20180626))
  2. Read- and locus-specific unique genome-wide 21mer filtering ( https://github.com/arangrhie/T2T-Polish/tree/master/marker_assisted overlapSelect -overlapBases=21)

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Data access

Raw RNA-seq data filled under BioProject PRJNA559484

Release history

  1. CHM13v2.0 assembly (minus chrY)

Credits

References

For generation of unique genome-wide 21mers:

For the RNA-seq experimental methods:

For the RNA-seq mapping and filtering methods: