Rsem

• convert-sam-for-rsem(1) Make a RSEM compatible BAM file.
• rsem-bam2wig(1) Convert BAM files to wiggle files.
• rsem-calculate-expression(1) Estimate gene and isoform expression from RNA-Seq data.
• rsem-control-fdr(1) Filter EBSeq output for statistical significance.
• rsem-generate-ngvector(1) Create Ng vector for EBSeq based only on transcript sequences.
• rsem-gff3-to-gtf(1) Convert GFF3 files to GTF files.
• rsem-plot-transcript-wiggles(1) Generate PDF wiggle plots from transcript or gene ids
• rsem-prepare-reference(1) Prepare transcript references for RSEM and optionally build BOWTIE/BOWTIE2/STAR/HISAT2(transcriptome) indices.
• rsem-run-ebseq(1) Wrapper for EBSeq to perform differential expression analysis.
• rsem-simulate-reads(1) Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.