if there is a low MAPQ in my reads . someone tells me to Use
samtools view in.bam "chr1:234-567" to explore the reads in the region of the gene.
he said : Your read counter might be refusing to count reads that do not align uniquely. this tool will let you count reads in the region, even if your read counter won’t assign them to a gene.
but i dont know how do it in galaxy ? im be grateful if someone can help me .
this is our conversation link : https://www.biostars.org/p/381880/