Hi,
I executed MIRA to assembly reads from a 454 (est assembly) but I obtained many
redundant contigs.
That is, when I ran a blastn of the contig set against itself, I saw results
like this:
Sequences producing significant
alignments: (bits) Value
assembly_rep_c1 975
0.0
assembly_rep_c402 957 0.0
assembly_rep_c1816 944 0.0
assembly_rep_c566 930 0.0
assembly_rep_c3933 924 0.0
assembly_rep_c343 914 0.0
assembly_c8340 906
0.0
assembly_c4763 900
0.0
assembly_rep_c1144 898 0.0
assembly_rep_c1247 878 0.0
assembly_c13612 874
0.0
assembly_c28064 870
0.0
assembly_c15892
866 0.0
assembly_rep_c9056
860
0.0
assembly_c14289
856 0.0
assembly_c10757
852 0.0
assembly_c27474
848 0.0
assembly_c16696
825 0.0
assembly_c23112
791 0.0
assembly_c16554
791 0.0
assembly_rep_c13107
777
0.0
assembly_c18699
761 0.0
assembly_c18498
761 0.0
assembly_c23851
731 0.0
I wonder what went wrong. I was thinking of reassembling the contigs (using
them as assembly input), but I'm not sure how to do it (which parameters should
I use in the job section. 454? sanger?) and if it is the right approach. Could
somebody help me?
Thank you very much.
Best regards,
Daniela.
