Hi,
I try to use Newbler 2.6 to reconstruct eucaryote transcriptome from 454 + Illumina SE data (100pb).
I made few test but it’s very long : 1 week for 500.000 reads 454 + 85 millions reads Illumina.
I run this command line :
/runAssembly -cdna -cpu 8 -mi 95 -ml 40 -urt fastq_file sff_file.
I have many problems :
1) Newbler recognize my fastq_file as a pairend fastq, while it is not the case. Anybody have a explanation?
2) Why the job is so long?
3) The parameter -ml 40 is it rigth? or I should try a other values?
Thank in advance,
I try to use Newbler 2.6 to reconstruct eucaryote transcriptome from 454 + Illumina SE data (100pb).
I made few test but it’s very long : 1 week for 500.000 reads 454 + 85 millions reads Illumina.
I run this command line :
/runAssembly -cdna -cpu 8 -mi 95 -ml 40 -urt fastq_file sff_file.
I have many problems :
1) Newbler recognize my fastq_file as a pairend fastq, while it is not the case. Anybody have a explanation?
2) Why the job is so long?
3) The parameter -ml 40 is it rigth? or I should try a other values?
Thank in advance,
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