Question: Whole exome: BAM statistics and other relevant information
0
gravatar for bioinf
2.7 years ago by
bioinf10
bioinf10 wrote:

Hi, 

I have paired-end bam files (exomes) for two groups each with multiple individuals (all from one species, non-viral). I am interested to get information as mentioned here http://www.ark-genomics.org/bioinformatics/virome  Would it be possible to do with `Rsamtools`? I am in the process of learning `Rsamtools` and getting stuck with how to process all files together to get final output. My aim is to retrieve genes and SNPs from this species as compared to reference (with same genus). Kindly guide.

Thanks!

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by bioinf10
1

Welcome! Can you ask a more specific question? Also, depending on what you are interested in, the GenomicAlignments (for a little more straight-forward data output data structures) package and GenomicFiles (for working with collections of BAM files) packages might be worth a look. Be sure to check out the vignettes.

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 23k

Thanks! I want to retrieve different parameters from bam files such as which chromosome from each file has most coverage, to look for specific genes etc. and then their plots as shown here http://www.ark-genomics.org/bioinformatics/virome

ADD REPLYlink written 2.7 years ago by bioinf10
Answer: Whole exome: BAM statistics and other relevant information
1
gravatar for Martin Morgan
2.7 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

The function idxstatsBam() summarized reads per sequence name quickly. I would not call this statistic 'coverage', but it would be sufficient for general QA or visualization purposes.

The rest of your question is too vague -- there is a ton of information at the URL you provide, and there is no magic bullet to produce all of it in a single command.

ADD COMMENTlink written 2.7 years ago by Martin Morgan ♦♦ 23k

Thanks! I can understand it is not the work of a single command but would it be possible with Rsamtools and in addition any other tools would you suggest (I am a beginner in exome analysis and there are so many tools available with no proper pipeline and  I want to use R-based).

ADD REPLYlink written 2.7 years ago by bioinf10
1

You have to figure out more precise questions to ask. I"ve mentioned the tools for very general analysis -- GenomicAlignments, GenomicFiles

ADD REPLYlink written 2.7 years ago by Martin Morgan ♦♦ 23k

Ok, thanks.

ADD REPLYlink written 2.7 years ago by bioinf10
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