Hello,
I am a new bfast user and have successfully run the full bfast job which included all the details. Now to speed up the processing (parallelize at various levels) at various steps I need to know the following from the authors and experts.
After using 10 unique set of indices suggested in the manual, I created 10 different index files.
refgenome.fa.cs.<j>.1.bif (j=1,..10).
I used the index files and the reference sequence and a unique reads.k.fastq file (k=1…N)
to <br>
search the indices (bfast index …)
perform local alignment (bfast localalign)
filter alignments (bfast postprocess)
1) My question is : Can I further parallelize the searches for indices (bfast index) step.
Can I run small jobs using independent index files for the above 3 steps and then merge the final *bam files after "bfast postprocess"?
2) how can I generate similar sized "reads.k.fastq" files . I noticed that some files generated are larger than others - perhaps twice as large. The compute time takes twice as long too.
Thanks in advance,
cheers
I am a new bfast user and have successfully run the full bfast job which included all the details. Now to speed up the processing (parallelize at various levels) at various steps I need to know the following from the authors and experts.
After using 10 unique set of indices suggested in the manual, I created 10 different index files.
refgenome.fa.cs.<j>.1.bif (j=1,..10).
I used the index files and the reference sequence and a unique reads.k.fastq file (k=1…N)
to <br>
search the indices (bfast index …)
perform local alignment (bfast localalign)
filter alignments (bfast postprocess)
1) My question is : Can I further parallelize the searches for indices (bfast index) step.
Can I run small jobs using independent index files for the above 3 steps and then merge the final *bam files after "bfast postprocess"?
2) how can I generate similar sized "reads.k.fastq" files . I noticed that some files generated are larger than others - perhaps twice as large. The compute time takes twice as long too.
Thanks in advance,
cheers
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