Combining Results of bam2seqz (parallel version)

[Erich Peterson]

Hi,

I am using the script suggested here to parallelize the execution of bam2seqz. As such, I have a seq.gz file for each chromosome. I am wondering if it is possible to combine them into one seq file before binning and using R to extract and visualize (on a genome wide basis)?

Thanks,

Erich

[Erich Peterson]

PS - Or I could combine after binning (so I could still use parallel methods to bin each seq file first).

[Francesco Favero]

Hi Erich,

Well it boils down to bash scripting at this point. I'm considering to write a tool for better manage the parallel thing, as I use it all the time (It speed up several time the process indeed...)

I usually keep the individual chromosomes seqz un-binned, then I concatenate the files with zcat gawk (to remove the extra headers and keep the first one) and pipe into the seqz binning tool and then gzip again.

If you don't care about the chromosome order it would be very straight forward, otherwise it's just a tiny bit longer.

if you need help I can give you more details.

Best

Francesco 

[Erich Peterson]

Thanks. Yeah, I was able to do something as you described.