Question: remove low number of reads from BAM file
0
gravatar for Mehmet
5.1 years ago by
Mehmet540
Japan
Mehmet540 wrote:

Dear All,

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

rna-seq alignment gene genome • 1.5k views
ADD COMMENTlink modified 5.1 years ago by Pierre Lindenbaum129k • written 5.1 years ago by Mehmet540

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

ADD REPLYlink written 5.1 years ago by Ashutosh Pandey12k

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.

ADD REPLYlink written 5.1 years ago by Mehmet540

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

ADD REPLYlink written 5.1 years ago by Mehmet540
2
gravatar for Pierre Lindenbaum
5.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

* 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.

ADD COMMENTlink written 5.1 years ago by Pierre Lindenbaum129k
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