This is a test version of Biostars. For the public version, visit https://www.biostars.org.
remove low number of reads from BAM file

Dear All,

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

alignment rna-seq genome gene
• 2,900 views • link
updated by Ram Ram • written by Mehmet Mehmet

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

• 0 views • link
written by Ashutosh Pandey Ashutosh Pandey

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.

• 0 views • link
updated by Ram Ram • written by Mehmet Mehmet

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

• 0 views • link
updated by Ram Ram • written by Mehmet Mehmet

1 answer

  • 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.
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this