Long-Read Isoform Identification with FLAIR
Isoform Identification in Apostichopus japonicus.
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.
Organism: Apostichopus japonicus.
Instrument: PacBio Sequel and Illumina HiSeq 2500.
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.
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.
PacBio NCBI Project: PRJNA785124.
Illumina NCBI Project: PRJNA687597.
NCBI Genome and Annotation: Apostichopus japonicus.
Long-Read Isoform Identification (FLAIR).
PacBio Long-Reads dataset in FASTQ format.
Aligned Short Reads in BAM format STAR.
NCBI genome in FASTA format.
Annotation File in GTF format.
Reads Manifest in TSV format to quantify final isoforms.
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
3 hours 23 minutes.
flair.transcriptome.gtf: Transcriptome Annotation in GTF format. It can be the input to SQANTI3.
flair.transcriptome.fa: Transcriptome Sequences in FASTA format.
flair.map.txt: Isoform-Read relationships.
flair.counts.tsv: Counts File of each discovered isoform.
flair_report.box: Summary Report
isoforms_length.box: Isoform Length Distribution