Hi everyone,
I got an exon level counts matrix (obtained via the Bioconductor recount3 package) and I would like to transform the exon counts to an estimation of transcript abundance.
Does anyone knows a way of doing this?
To convert exon-level counts to transcript-level quantification in RNA-seq data analysis, obtain a transcript annotation file in GTF or GFF format. Aggregate exon counts to transcript level using tools like featureCounts or HTSeq-count. Normalize transcript counts to account for sequencing depth and library size using methods like TPM or FPKM. Filter out lowly expressed transcripts or those with low counts and annotate transcripts with gene names and functional information if needed.
Dear Susanta,
as far as I know, htseq and featureCounts take only sam/bam files as inputs (i.e., alignment files).
What I got is a count matrix on exon level. What I need is a summarization/quantification on transcript level. Or do you know a way to make these counting tools taking count matrices as input?
Best regards
Markus
You might try using snapcount, tximport R package to summarize transcript-level abundance estimates.
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