Hi Group,
I am a relative newbie tying to come upto speed. So I managed to assemble a 20 core cluster and am just beginning to figure out how to work the bioinformatics assembly algorithms. So my scenario is this
1) I currently have a WES raw data file measuring 5 GB. I have a quality score file which is approximately 12 GB.
2) I have a four node AMD cluster with 32 GB RAM. I installed and configured Rocks software on the same.
3) I have been looking into Bowtie to do the analysis on this cluster.
Some questions which come to my mind are as follows
1) How and where do I start?
2) Is it possible to install bowtie on the ROCKS cluster such that I can use the 4 nodes to run the analysis in parallel?
3) For this single massive file of 5 GB raw reads, how do I go about doing the assembly?
4) With bowtie, am I restricted to using only ONE node on which to run the analysis on?
5) OR, can I split my raw reads of file X4 and farm out each file to each one of the nodes and do the assembly and then do a final assembly of all the four assembled files?
6) Has anyone installed Galaxy tools on a ROCKS cluster? Could you share your experiences of the same?
I realize these are very basic and fundamental questions. But I would highly appreciate an answer. Hopefully I will be able to answer these questions on the forum in the near future.
Regards
Quantrix
I am a relative newbie tying to come upto speed. So I managed to assemble a 20 core cluster and am just beginning to figure out how to work the bioinformatics assembly algorithms. So my scenario is this
1) I currently have a WES raw data file measuring 5 GB. I have a quality score file which is approximately 12 GB.
2) I have a four node AMD cluster with 32 GB RAM. I installed and configured Rocks software on the same.
3) I have been looking into Bowtie to do the analysis on this cluster.
Some questions which come to my mind are as follows
1) How and where do I start?
2) Is it possible to install bowtie on the ROCKS cluster such that I can use the 4 nodes to run the analysis in parallel?
3) For this single massive file of 5 GB raw reads, how do I go about doing the assembly?
4) With bowtie, am I restricted to using only ONE node on which to run the analysis on?
5) OR, can I split my raw reads of file X4 and farm out each file to each one of the nodes and do the assembly and then do a final assembly of all the four assembled files?
6) Has anyone installed Galaxy tools on a ROCKS cluster? Could you share your experiences of the same?
I realize these are very basic and fundamental questions. But I would highly appreciate an answer. Hopefully I will be able to answer these questions on the forum in the near future.
Regards
Quantrix
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