Map RNA-Seq reads in 3' UTR region

Question

[luca]

Hi folks, I just have a quick question which hopefully has a simple answer. I downloaded from NCBI a set of fastq files containing mouse RNA-seq data which was generated using "classic" TruSeq RNA-library preparation kit. Hence it contains reads from the whole mRNA molecule. I want to align (and then count) reads that do map only the 3' UTR region. I am currently using STAR to map the reads and the star index was built with the latest Ensembl .gtf and .fasta files.

Any suggestion will be much appreciated Thanks Luca

Answer 1

[ATpoint]

The 3'UTRs should be annotated in the reference GTF/GFF3 file which you can filter for the coordinates. Once you have the coordinates use something like samtools view with the aligned bam file:

samtools view -L BEDfile_with_3UTRcoordinates.bed -o data_3UTR_reads.bam aligned.bam

[luca]

Thanks ATpoint for your reply. How do I extract the coordinates of UTR regions from the GTF file?

[ATpoint]

See for general inspiration: A: how to get intronic and intergenic sequences based on gff file?

[luca]

Thanks! I will have a look at it!