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Overview

The sections of ISOdb contain Home, Browse, Search and Download pages. The navigation bar provides a quick access to the help file of each main section.

Home

Browse

The Browse page provides a comprehensive display of Iso-Seq data in three different dimensions: (1) Iso-Seq reads information; (2) The isoform composition and distribution in genes (3) The alternative splicing (AS) statistics in isoform.

Search

Select a species and enter a gene name in the search box of the search page, the output shows the total isoform, novel isoform number and alternative splicing (AS) number of the gene. The JBrowse icon provides hyperlink to a genome browser, which query and visualize context-specific Iso-Seq data. The total isoform number can be linked to the detailed isoform information.

Data processing

The Iso-Seq datasets were processed and analyzed by the above unified pipeline. The detailed data processing in the pipeline is as follows: First, the raw sequence files produced from PacBio (bax.h5) were extracted and reads of insert (known as circular consensus sequence, CCS) were generated using ConsensusTools.sh. Subsequently, the reads were classified into full-length and non-full-length reads using pbclassify.py. The full-length reads were fed into the isoform-level clustering (ICE), and all the results were polished using Quiver. Finally, we aligned the quivered fasta sequences against each reference genome by using GMAP, and analysed the spliced isoforms with TAPIS and SpliceGrapher by using the annotation file.

The reference genomes for alignment in species are listed as follows:

Species Reference Link

Contact

If you have any questions or comments, please contact us.

Shang-Qian Xie
sqianxie@gmail.com

Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China

Chuan-Le Xiao
xiaochuanle@126.com

Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China