Question: Getting pileup information from Sam files
gravatar for anjali.gopal91
6.1 years ago by
United States
anjali.gopal9150 wrote:

I'm working on a project where I'm aligning fastq files that contain sequence information about a series of small ORfs (usually ~2 kb in size). These were all contained in bacterial entry vectors (i.e., plasmids).

I'm using bowtie2 to align these sequences, but would like to determine the pileups somehow.

Currently, I've tried using mpileup with samtools. However, since samtools works with diploid genomes, my questions are:

1) Would using samtools mpileup to determine pileup information be incorrect for a haploid organism? (Note that I'm not doing variant calling; I use SNVer to do variant calls).
2) If so, is there another program I can use to get pileup info for haploid organisms? Alternatively, is there anything I can do in samtools to specify ploidy? It doesn't seem to be an option right now.



ADD COMMENTlink modified 6.1 years ago by Devon Ryan96k • written 6.1 years ago by anjali.gopal9150
gravatar for Devon Ryan
6.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

The pileup itself will be the same regardless of the organism's ploidy. So as long as you're not depending on samtools to call the variants then you shouldn't have any issues.

ADD COMMENTlink written 6.1 years ago by Devon Ryan96k
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