Mohd Murshad Ahmed
@murshadahmedI am a Postdoctoral Fellow at Albert Einstein College of Medicine, New York, USA. My area of expertise is scRNA/snRNA analysis.
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Alternative polyadenylation can occur in introns, termed intronic polyadenylation (IPA), has been implicated in diverse biological processes and diseases, as it can produce noncoding transcripts or transcripts with truncated coding regions
The visualization of full-length transcripts, especially when there are many isoforms per gene, can be a challenge.Swan is a long-read visualization tool that can plot expression or percent isoform values of each transcript in a gene alongside the transcript’s actual model. It also performs statistical tests to find isoform-switching genes.
pbfusion is a breakpoint-centric fusion gene caller. It uses mapped Iso-Seq reads and reference gene annotations to identify transcript breakpoints between genes and also provides visualization scripts.
BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis evaluates genome assembly and annotation completeness by identifying highly conserved, single-copy genes across specific lineages. It classifies genes as Complete (Single or Duplicated), Fragmented, or Missing to quantify quality, providing a standard for assessing genomic data
Iso-Seq reads ↓ Isoform detection ↓ SQANTI3 annotation ↓ Isoform quantification ↓ Expression matrix ↓ Isoform → gene mapping ↓ Isoform usage calculation ↓ Isoform switching analysis ↓ Top switching genes (Rgs8, Bhmt2, Myh9, ...)
we use SQANTI3 for annotation
RNA-Bloom2 Analysis using the brain data of Degus. Denovo Assembly code
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