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.
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.
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:
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Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China