I want to remove low number of reads from alignment BAM file. How can I do that?
Please elaborate what you mean by "low number of reads". Are these reads with low mapping quality ?
Hi, I am looking my alignment file on Artemis. I have seen low mapping quality (low number of reads per an exon). I don't know how to explain this. For example, There is only one read per an exon, which affects my gene statistics obtained by using RNAseq hints. I used Augustus for gene prediction.
Hi again, I want to remove low coverage maps from BAM file. How can I do that?
* use GATK depthofcoverage to get the coverage of the bam
* get a BED file of the high-cov regions
* use samtools view to extract the reads overlaping the BED file.