Hi,
I would like to ask for an advice:
I have an RNA-seq bam-file and i have to count the exonic reads and intronic reads for each annotated refseq transcript.
So, in the end I would like to have a table of something like this:
Could somebody please tell me a simple way to count reads on summa exons and summa introns for each transcripts? ( for each refseq gene ?)
I was thinking about this method:
First splitting the bam.file into only exonic reads and intronic reads using:
Then count reads on each gene from each intron/exon.bed file separately.
(however i am afraid that the exon-exon junction reads will be counted twice by this way... right?)
Thank you in advance for the help.
If i happened to miss an existing thread about this/similar problem, please let me know.
I would like to ask for an advice:
I have an RNA-seq bam-file and i have to count the exonic reads and intronic reads for each annotated refseq transcript.
So, in the end I would like to have a table of something like this:
name - - - reands on exons - - - reads on introns
nm_00001 - - - 3214 - - - 1025
nm_00001 - - - 3214 - - - 1025
I was thinking about this method:
First splitting the bam.file into only exonic reads and intronic reads using:
Code:
bedtools intersect -split -bed -a bam.file -b exonscoordinates.bed > exonicreads.bed bedtools intersect -split -bed -a bam.file -b intronscoordinates.bed > intronicreads.bed
(however i am afraid that the exon-exon junction reads will be counted twice by this way... right?)
Thank you in advance for the help.
If i happened to miss an existing thread about this/similar problem, please let me know.
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