Long-Read Isoform Identification with FLAIR

Introduction

Isoform Identification in Apostichopus japonicus.

Dataset Description

This dataset contains one file of long reads sequenced by PacBio Sequel technology and two BAM files generated using STAR from two pairs of paired-end FASTQ files with short reads sequenced by Illumina HiSeq 2500 technology.

Publication

Wang, Y., Yin, Y., Cong, X., Storey, K.B. and Chen, M., 2022. PacBio Isoform Sequencing and Illumina RNA Sequencing Provide Novel Insights on Responses to Acute Heat Stress in Apostichopus japonicus Coelomocytes. Frontiers in Marine Science, 8, p.815109.

 Abstract

Significant increases in global sea surface temperatures are expected with climate change and may cause a serious challenge for marine organisms cultured in aquatic environments that are characterized by short and long-term fluctuations in water temperatures. Apostichopus japonicus, a sea cucumber with high nutritional value and pharmacological properties, is an important economic species that is widely raised in aquaculture in China. In recent years, continuous extreme high temperatures (up to 30°C) have occurred frequently in summer leading to mass mortality of sea cucumbers cultured in semi-open shallow regions seriously restricting the sustainable development of sea cucumber aquaculture. In the present study, we combined RNA-seq and PacBio single-molecular real-time (SMRT) sequencing technology to unveil the potential mechanisms of response to acute heat stress in A. japonicus coelomocytes. A total of 1,375 differentially expressed genes (DEGs) were identified in a comparison of control and 48 h heat stress (HS) groups.

Original Data

Bioinformatic Analysis

Application

Long-Read Isoform Identification (FLAIR).

Input

Parameters

  • Use Own Alignment Files: false

  • Use Short Reads: True

  • Quantify Reads: false

  • Native RNA: false

  • Minimum Mapping Quality: 1

  • Retain Secondary Alignments: 0

  • Window Size: 15

  • Minimum Supporting Reads: 3

  • Window Size for TSS and TTS: 100

  • Ends Determined at Isoform Level: false

  • Use Supporting Reads for TSS/TTS: false

  • How to Treat Redundant Isoforms: No redundancy control

  • How to Filter Isoforms: Filter based on support

  • Minimum Mapping Quality: 1

  • Stringent Mode: false

  • Check Splice Sites: false

  • Trust Ends: false

Execution Time

3 hours 23 minutes.

Output

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