TBProfiler

Setting up with premade BAMs

Create a folder to hold the project:

mkdir tbprofiler
cd tbprofiler
mkdir bam

Move all your bam files to the bam directory

Create a list of samples using the BAM files

cd bam
ls *.bam | sed 's/.bam//' > ../samples.txt
cd ../

Running TBProfiler

Now you are ready to run the TBProfiler. Here is an example:

cd merged

~/TBProfiler/tb-profiler full -a bam/<prefix>.bam -p <prefix> -t 4

Replace <prefix> with whatever sample name you have given to your bams

To see the results from the analysis:

cat results/<prefix>.results.txt

If you want to run the profiler for all the bamfiles:

cat samples.txt | xargs -i sh -c "echo Processing {}; ~/TBProfiler/tb-profiler full -a bam/{}.bam -p {} -t 4"

More info

You can find more info here.