Dear boetsie,
On another note, for my -x 0 output, I am noticing that an 'n' is being reported instead of lower case nt's when there is a clear overlap between adjacent contigs in the scaffold output.
For example, the first two contigs of a scaffold are:
>contig29
....TTCTTTTTCTTCCCATCTTCAGCCTTCTTAGCTTCGGCTTCCTCCCTCTCTTTCAACACAACAAGGGCAT
>contig15
TTCTTTTTCTTCCCATCTTCAGCCTTCTTAGCTTCGGCTTCCTCCCTCTCTTTCAACACAACAAGGGCAT....
There is a clear 70nt overlap, however the final.scaffold output is putting an 'n' between these two contigs. This the details of the scaffold:
>scaffold1.1|size6918|tigs5
f_tig29|size803|links11|gaps-58
f_tig15|size4884|links6|gaps-99
f_tig13|size173|links6|gaps-24|merged38
f_tig24|size387|links45|gaps-52|merged45
f_tig8|size752
However it is reporting lowercase nts between contig 13/24 and 24/8, so I'm wondering if there is some kind of threshold '-n' which determines what is reported.
My invocation was:
perl /usr/local/bin/SSPACE-1.1_linux-x86_64/SSPACE_v1-1.pl -l library.txt -s contigsassem71.fa -x 0 -m 50 -o 20 -n 15 -p 1 -v 1 -b pass11_sspace
Sorry for the spate of questions.
Thanks!
Kennels
On another note, for my -x 0 output, I am noticing that an 'n' is being reported instead of lower case nt's when there is a clear overlap between adjacent contigs in the scaffold output.
For example, the first two contigs of a scaffold are:
>contig29
....TTCTTTTTCTTCCCATCTTCAGCCTTCTTAGCTTCGGCTTCCTCCCTCTCTTTCAACACAACAAGGGCAT
>contig15
TTCTTTTTCTTCCCATCTTCAGCCTTCTTAGCTTCGGCTTCCTCCCTCTCTTTCAACACAACAAGGGCAT....
There is a clear 70nt overlap, however the final.scaffold output is putting an 'n' between these two contigs. This the details of the scaffold:
>scaffold1.1|size6918|tigs5
f_tig29|size803|links11|gaps-58
f_tig15|size4884|links6|gaps-99
f_tig13|size173|links6|gaps-24|merged38
f_tig24|size387|links45|gaps-52|merged45
f_tig8|size752
However it is reporting lowercase nts between contig 13/24 and 24/8, so I'm wondering if there is some kind of threshold '-n' which determines what is reported.
My invocation was:
perl /usr/local/bin/SSPACE-1.1_linux-x86_64/SSPACE_v1-1.pl -l library.txt -s contigsassem71.fa -x 0 -m 50 -o 20 -n 15 -p 1 -v 1 -b pass11_sspace
Sorry for the spate of questions.
Thanks!
Kennels
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