STAR

Align RNA-seq reads to the reference genome using STAR.

Generate read counts per gene using tools like HTSeq or featureCounts.

Normalize read counts to account for library size and gene length.

Perform differential expression analysis using DESeq2 or edgeR.

Align RNA-seq reads to the reference genome using STAR with splice junction discovery enabled.

Assemble transcripts using tools like StringTie or Cufflinks.

Compare assembled transcripts to known annotations to identify novel isoforms.

Validate novel isoforms using RT-PCR or other experimental methods.

Align RNA-seq reads to the reference genome using STAR.

Mark duplicate reads using Picard or similar tools.

Perform base quality score recalibration using GATK.

Call variants using tools like GATK HaplotypeCaller or FreeBayes.

Align RNA-seq reads to the reference genome using STAR with specific parameters for chimeric alignment.

Filter chimeric alignments based on mapping quality and other criteria.

Annotate chimeric junctions using databases like ChimerDB or COSMIC.

Validate fusion genes using PCR or other experimental methods.

Align RNA-seq reads to the reference genome using STAR.

Identify mismatches between RNA-seq reads and the reference genome.

Filter mismatches based on quality scores and other criteria.

Annotate RNA editing sites using databases like RADAR or DARNED.