remove low number of reads from BAM file

Question

[Mehmet]

Dear All,

I want to remove low number of reads from alignment BAM file. How can I do that?

[Ashutosh Pandey]

Please elaborate what you mean by "low number of reads". Are these reads with low mapping quality ?

[Mehmet]

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.

[Mehmet]

Hi again, I want to remove low coverage maps from BAM file. How can I do that?

Answer 1

[Pierre Lindenbaum]

• 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 overlapping the BED file.