feature count
Budget: ₹1,500 – ₹12,500 INR
Data Preparation: Ensure you have the necessary data, including RNA-seq raw reads (usually in FASTQ format), a reference genome, and an annotation file (often in GTF or GFF format) that defines genomic features.
Alignment: Align your RNA-seq reads to the reference genome using a suitable alignment tool like HISAT2, STAR, or Bowtie2. This step generates alignment files in formats like BAM or SAM.
Feature Counting Tool: Use a feature counting tool to quantify the number of reads that align to genomic features. Popular tools include Subread's featureCounts, HTSeq, or the count function in R packages like GenomicAlignments or DESeq2.
Specify Annotation File: Provide the annotation file (GTF or GFF) to the feature counting tool. This file defines the genomic features you want to count reads for, such as genes or exons.
Counting Reads: Run the feature counting tool, specifying the aligned BAM/SAM files and the annotation file. It will generate a count table that lists the number of reads associated with each genomic feature.
Alignment: Align your RNA-seq reads to the reference genome using a suitable alignment tool like HISAT2, STAR, or Bowtie2. This step generates alignment files in formats like BAM or SAM.
Feature Counting Tool: Use a feature counting tool to quantify the number of reads that align to genomic features. Popular tools include Subread's featureCounts, HTSeq, or the count function in R packages like GenomicAlignments or DESeq2.
Specify Annotation File: Provide the annotation file (GTF or GFF) to the feature counting tool. This file defines the genomic features you want to count reads for, such as genes or exons.
Counting Reads: Run the feature counting tool, specifying the aligned BAM/SAM files and the annotation file. It will generate a count table that lists the number of reads associated with each genomic feature.