HTSeq-count annotation and abundance count of exons from a cDNA composite
We have 6 muscle types with 4 specific exons that look to be alternatively spliced are present in each muscle type.
We have paired-end Illumina RNASeq reads and we are working with a non-model organism with no reference genome. We have a working composite for a protein sequence that includes every exon we have found via cDNA.
As I understand it, Htseq-count finds the exons that reads overlap with and then groups counts based on the exon's gene ID in the GTF file. How do annotate my composite to show me the abundance at which theses 4 exons are expressed?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Merge 2 GTF using agat avoiding overlapping
written by Rafael Soler •
-
Is there a straightforward way to use RNA alignment with the genome to infer exon-intron structure?
written by charleslindberg976 •
-
which feature type and id attribute to use in ht-seq count
written by kousi31 •
-
Adding annotation into a transcript in order to use TopHat2
written by mlopez •
-
Abundance/frequency of RNASeq raw reads mapped to a transcript exon
written by mlopez •
-
Get an abundance/frequency of how many times within an RNASeq file a transcript maps to an exon
written by sdbaney •
-
How to count the reads that overlap with 3' splice sites or 5' splice sites?
written by vaslanzadeh •
-
Testing for over-representation of chip-peaks
written by Bioradical •
-
Annotating RNA-Seq exon junctions
written by george.wiggins •
-
Rna-Seq Raw Counts
written by Gregor Rot
