UW Iso-Seq Track Settings
 
University of Washington Iso-Seq Mappings   (All mRNA and EST tracks)

Display mode:       Reset to defaults

Display read names
Minimum alignment quality:

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
Use R,G,B colors specified in user-defined tag
No additional coloring

Display data as a density graph:

BAM configuration help

All subtracks:
List subtracks: only selected/visible    all    ()  
 
hide
 Configure
 Iso-Seq Cerebellum (2)  UW Iso-Seq Cerebellum SRR11734396 (SMRTCell 2)   Schema 
 
hide
 Configure
 Iso-Seq Cerebellum (3)  UW Iso-Seq Cerebellum SRR11734396 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Hippocampus (1)  UW Iso-Seq Hippocampus SRR11734177 (SMRTCell 1)   Schema 
 
hide
 Configure
 Iso-Seq Hippocampus (3)  UW Iso-Seq Hippocampus SRR11734177 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Prefrontalcortex (1)  UW Iso-Seq Prefrontalcortex SRR11734138 (SMRTCell 1)   Schema 
 
hide
 Configure
 Iso-Seq Prefrontalcortex (3)  UW Iso-Seq Prefrontalcortex SRR11734138 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Striatum (1)  UW Iso-Seq Striatum SRR11735653 (SMRTCell 1)   Schema 
 
hide
 Configure
 Iso-Seq Striatum (3)  UW Iso-Seq Striatum SRR11735653 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Thalamus (2)  UW Iso-Seq Thalamus SRR11734242 (SMRTCell 2)   Schema 
 
hide
 Configure
 Iso-Seq Thalamus (3)  UW Iso-Seq Thalamus SRR11734242 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Visualcortex (1)  UW Iso-Seq Visualcortex SRR11734146 (SMRTCell 1)   Schema 
 
hide
 Configure
 Iso-Seq Visualcortex (3)  UW Iso-Seq Visualcortex SRR11734146 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Heart (2)  UW Iso-Seq Heart SRR11734243 (SMRTCell 2)   Schema 
 
hide
 Configure
 Iso-Seq Heart (3)  UW Iso-Seq Heart SRR11734243 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Kidney (2)  UW Iso-Seq Kidney SRR11734145 (SMRTCell 2)   Schema 
 
hide
 Configure
 Iso-Seq Kidney (3)  UW Iso-Seq Kidney SRR11734145 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Liver (1)  UW Iso-Seq Liver SRR11734136 (SMRTCell 1)   Schema 
 
hide
 Configure
 Iso-Seq Liver (3)  UW Iso-Seq Liver SRR11734136 (SMRTCell 3)   Schema 
 
hide
 Configure
 Iso-Seq Muscle (2)  UW Iso-Seq Muscle SRR11734395 (SMRTCell 2)   Schema 
 
hide
 Configure
 Iso-Seq Muscle (3)  UW Iso-Seq Muscle SRR11734395 (SMRTCell 3)   Schema 
    

Description

These tracks show the Iso-Seq long read alignments of marmoset cDNAs to the genome. The data set consists eleven tissue samples from two individuals.

Display Conventions and Configuration

These track use the BAM Display Conventions and Configuration.

Methods

  1. Generation of Full Length cDNA and Library Preparation for Sequencing

    Full-length cDNA was prepared and sequenced from total RNA isolated from various tissues of both a two year old male and a two year old female Callithrix jacchus. Iso-Seq library production was performed as per the Iso-Seq Express protocol (https://www.pacb.com/wp-content/uploads/Procedure-Checklist-IsoSeq-Express-Template-Preparation-for-Sequel-and-Sequel-II-Systems.pdf) and barcoded using barcoded adapters. One library was generated for each tissue.

  2. Sequencing with the PacBio Sequel II Platform

    Libraries were pooled equimolar and sequenced on 3 SMRT Cell 8M on the Sequel II platform with chemistry version 2EA.

  3. Data Processing

    Collected data was demultiplexed with lima (demultiplex barcoding), then analyzed with CCS with a requirement of 1 minimum pass and at least 0.9 identity (--minPasses 1 --min-rq 0.9). The Iso-Seq analysis pipeline was used to generate FLNC reads ensuring each has a poly-A tail, plus a single 3' and 5' primer signal for downstream analysis.

  4. Mapping

    Resulting reads were aligned to the marmoset genome with minimap2 2.17-r941 using the options -t 12 -ax splice:hq -u.

Data Access

The genomic alignments are stored in a BAM file that can be obtained from the download server.

Credits

Samples were provided from the New England Primate Research Center by Ricardo del Rosario and Anna Newman of the Broad Institute.

Iso-Seq sequencing & FLNC analysis performed by: Evan Eichler, Alexandra Lewis, Shwetha Murali, and Katherine Munson of the University of Washington.

References

Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW et al. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science. 2020 Dec 18;370(6523). PMID: 33335035; PMC: PMC7818670