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