Question: samtools vs bedtools
gravatar for xupbuy
18 months ago by
xupbuy10 wrote:

Hi I have a silly question: What is the difference between samtools depth and bedtools genomecov? For both tools, the input file needs to be *.sorted.bam, which was generated by sam->bam->sorted.bam.

I tried both tools using the same *.sorted.bam input file and they generate the same coverage file.

Another question:

Can I use bedtools to map reads file (fastq or fasta ) to a reference genome? Like bowtie or bwa did? Because I like the function of bedtools that gives you how many reads map to the genome, and also the percentage of genome that is mapped by the reads.

Thank you.

sequencing alignment • 952 views
ADD COMMENTlink modified 18 months ago by genomax68k • written 18 months ago by xupbuy10

No, you cannot use bedtools as an aligner in any meaningful way.

ADD REPLYlink written 18 months ago by jared.andrews072.5k

Your question is not silly, but is poorly formulated, and suggests you made little effort to find the answers. For example, samtools depth vs bedtools genomecov has been discussed many times (e.g. avrilomics blog, on biostars or bioinformatics stackexchange). Please read Tutorial: How To Ask Good Questions On Technical And Scientific Forums.

ADD REPLYlink written 18 months ago by h.mon26k
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