Run blat on multiple processor cores

[mizar106]

Hi guys!
I'm completely new in the NGS-community! I'm interested obviously in NGS-data analysis but still not very familiar with a series of technical issues normally encountered in this field.
In particular, my problem now is that I have to run blat-mapping of a fasta file on the whole human genome (1 different fasta per chromosome). Since I work just only with my own machine (having 16 cores in total) I was trying to find an efficient method/strategy to split each blat job on multiple cores on the machine. Concerning this, I found and tested GNU-parallel but after one complete day of tests it does not work. does somebody know how to use that or maybe some other strategy to split every single job (I will have 1 job = 1 chromosome) on multiple cores? For me it seems a bit difficult to solve this.
Thanks a lot in advance!!!!

[GenoMax]

How much memory do you have? Remember that blat keeps entire reference index in memory so if you start 16 parallel jobs each may need a copy in memory (in case GNU-parallel truly treats these as separate jobs, I am not familiar with that part).

When you say "it does not work" what is exactly happening? Errors?

[mizar106]

How much memory do you have? Remember that blat keeps entire reference index in memory so if you start 16 parallel jobs each may need a copy in memory (in case GNU-parallel truly treats these as separate jobs, I am not familiar with that part).

When you say "it does not work" what is exactly happening? Errors?

Hi, thank you fot the answer!
Actually the 'parallel' program didn't work properly because I didn't understand the correct arguments of GNU parallel to specify into the command line with blat , but finally I was able to find the correct command and It works. The problem from what I understood about GNU-parallel is that it allows to run simultaneously multiple jobs such a way that 1 job runs on 1 core..but this is not really what I need, unfortunately. I'm looking for a way to run a single job on multiple cores (lika to 'split' the job let's say). I have a machine with 2 Intel Xeon processors equiped with 8 cores each one (but in the monitoring system dialog I see 32 cpus in total, maybe beacuse threads are 2 x each core?), the RAM is 64Gb in total.
Thanks for any help.

[GenoMax]

A search brings up this: http://code.google.com/p/pblat/ I have not personally used it but you may want to give it a try.

[mizar106]

A search brings up this: http://code.google.com/p/pblat/ I have not personally used it but you may want to give it a try.

Seems to be interesting! thanks a lot!!!

[jp.]

Hi all
I m doing exome seq mutation using PICAR+GATK followed by annovar. I have successfully completed the pipelines and got my resuts. However, I want to filter out my SNPs using blat??
can some one help me or guide me on how to filter out failed blat SNPs using blat ?
thank you in advance