Hi,

I'm looking for a nice way to calculate the percentage of reads on specifique chromosomes (MT und (1-23,X,Y) und unplaced scaffold).

 I know I can get the read counts per chromosome with `samtools idxstats`, however I have a lot of bam files and I would like to automate the calculation. The problem is, I'm struggling with basic batch text maniplulation and would therefore appreciate any help you can give me (specific or general).

Edit: I forgot to mention, that I have multiple bam files, which are indexed and only consist of uniquely mapped reads.
General workflow you could try given that you use R.

1. Look at using `dir()` to get a list of index files.
2. Look at using `sprintf()` to create a command string to run samtools idxstats given a filename (which you have from #1), piping the results to a unique file for each sample.
3. Look at using `system()` to run the command string from 2.
4. Look at using a for loop loop to run #3 over your list of index files from #1.
5. Define a function to read a single idxstats output file.
6. Loop using sapply or lapply over all the idxstat output files
7. Combine output of 6 into a single matrix, with samples in columns and chromosomes in rows.

