Question: How to use "Mpileup" for getting information of the reads of the SNP from the BAM files?
0
gravatar for jigarnt
6 months ago by
jigarnt30
Canada
jigarnt30 wrote:

Hi All,

I am thinking of using Mpileup from Samtools to get the information on the read quality and read depth from the BAM files. In that case which script should I use?

I have been recommended the script below:

ref=my_fasta.fasta samtools mpileup -f $ref -r chromosome_1:1018000-1018100 my_bam.bam my_bam2.bam

P.S. I dont have to do Variant calling, just need the read information.

Thanks in advance for your help.

mpileup snp bam genome • 332 views
ADD COMMENTlink modified 6 months ago by agata88440 • written 6 months ago by jigarnt30
0
gravatar for agata88
6 months ago by
agata88440
Poland
agata88440 wrote:

I would not use mpileup at all - if you need only alignment statistics. Use BedTools. For example here : A: How to get coverage for an alignment file The read quality you can get from FASTQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

But to be clear:

First what you should do is to check your reads by FASTQC (if the quality is bad do trimming), then align them to reference and then perform BedTools.

Best,

Agata

ADD COMMENTlink written 6 months ago by agata88440
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