RNAseq default Track Settings
 
CHM13 RNAseq Bowtie2 default mapped (chm13v1.1) and unique genome-wide kmer filtering   (All Transcription tracks)

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dense
 Configure 		 RNAseq-A bt2-dflt  RNAseq-A bt2 default no kmer filtering   Schema 
dense
 Configure 		 RNAseq-A bt2-dflt-21mer  RNAseq-A bt2 default 21mer filtering   Schema 
dense
 Configure 		 RNAseq-A bt2-dflt-51mer  RNAseq-A bt2 default 51mer filtering   Schema 
dense
 Configure 		 RNAseq-B bt2-dflt  RNAseq-B bt2 default no kmer filtering   Schema 
dense
 Configure 		 RNAseq-B bt2-dflt-21mer  RNAseq-B bt2 default 21mer filtering   Schema 
dense
 Configure 		 RNAseq-B bt2-dflt-51mer  RNAseq-B bt2 default 51mer filtering   Schema 
    

Description

CHM13 RNA-seq Bowtie2 default alignments and Meryl unique k-mer filtering

Methods

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

Display Conventions and Configuration

Data access

Release history

  1. CHM13v1.1 assembly (04.27.21)

Contacts

Credits

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)