Hello people!
I am doing a de novo transcriptome assembly and after reading the literature I went for Oases. Even though it seemed to give very good results, I am not getting really good values for my assemblies.
The max contig length is very low (highest is around 7000 for kmer , but after the oases merge this value always drops down to around 2500 tops.
Also, the N50 values are very low (between 26 and 200). The kmer interval that I am using is between 17 and 65, step of 8. The cov_cutoff is of 5 and the merging kmer 27. I started with very high quality illumina reads (100 bp) and 80 bp insert length.
Could anyone give me some tips on the assembly, and why am I getting really small contigs? Also, I am struggling with the runs, since they are taking several days do finish (7 days, 10 core 50 g per core).
Finally, I want to re-run Oases on the Velvet runs, but change the kmers. Can I do that? For instance, after running with the python script with a kmer interval of 17-65, do another merge with the runs from the kmer interval 25 - 55.
Many thanks in advance!!
Susana
I am doing a de novo transcriptome assembly and after reading the literature I went for Oases. Even though it seemed to give very good results, I am not getting really good values for my assemblies.
The max contig length is very low (highest is around 7000 for kmer , but after the oases merge this value always drops down to around 2500 tops.
Also, the N50 values are very low (between 26 and 200). The kmer interval that I am using is between 17 and 65, step of 8. The cov_cutoff is of 5 and the merging kmer 27. I started with very high quality illumina reads (100 bp) and 80 bp insert length.
Could anyone give me some tips on the assembly, and why am I getting really small contigs? Also, I am struggling with the runs, since they are taking several days do finish (7 days, 10 core 50 g per core).
Finally, I want to re-run Oases on the Velvet runs, but change the kmers. Can I do that? For instance, after running with the python script with a kmer interval of 17-65, do another merge with the runs from the kmer interval 25 - 55.
Many thanks in advance!!
Susana
Comment