CDS read counts per gene
Hi Guys,
I have aligned RNA-seq data and have bam files. I am goint to coundt the number of reads per gene but I need only the number of reads per gene only for coding sequence part of genes. do you guys know how to get those counts? tHANKS
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Exon and junctions count per gene
written by rhonddaskl •
-
gene sequence fetching from bam or fastq file of rna seq data
written by fatimarasool135
-
counting the reads mapped to specific coordinate in the genome
written by alirezamomeni707 •
-
extracting 5'UTR of each gene
written by ashkan
-
optimum statistical test to get significance level
written by ashkan
-
problem with counting reads per gene using HTseq
written by ashkan
-
coding sequnce read coun
written by ashkan
-
Ribo-seq vs RNA-seq read count
written by ashkan
-
upstream open reading frame gene filteration
written by ashkan
-
filtering out the genes in RNA-seq experiment
written by ashkan
Dear Behzad, Hi
Does this post can offer any helps to you ?
And I guess if you have GTF file there would be some transcripts coordinates such as CDS in it.
~Best
If I understand correctly, he needs counts, not reads. This is exactly what featureCounts or htseq-counts does. "Counting reads per annotation element".
Dear @Wouter, Hi.
Do you mean this and this ?
Yes, as such he can "count the number of reads per gene" -> as he asked for ;-)