I have a specific genomic region saved as fasta. I want to check how many reads mapped to this specific region and extract them, as for example .bam file.
I used RMTA tool (github link) to map RNA-seq reads to the specific region (so instead of mapping reads to a whole genome I mapped reads only to the specific region).
I used specifically command:
sudo docker run --rm -v $PWD:/data -w /data evolinc/rmta:2.6.3 -g \
specific_region.fasta -l "US" -n 1 -y "PE" -1 \
R1.fastq -1 R2.fastq -2 final_out -p 10 \
-5 0 -3 0 -m 20 -M 50000 -t -u "exon" -a "gene_id" -n 1 -f 1 -k 1
As an output I obtained the .bam file, but with all reads (not only mapped ones).
Next, I visualized it in IGV, where I can clearly see properly mapped reads to my region, but I do not know how to extract them.
I couldn't see any "filtering" option in RMTA, which allows for creating .bam only from mapped reads.
Is it some other way to extract only reads mapped to the specific region preferably as .bam?
