How to reproduce the communities in your article?

[kikegoni]

Hey!

First thanks a los for implementing SEEKR, I find it really useful!!

I am trying to analyze the similarity between some lncRNAs and I have started by trying to run SEEKR on all lncRNAs from GENCODE in order to check that I obtain the same communities that you have found in the Supplementary Table 7 of you paper.
However, even though I find some agreement, the results I have obtained do not totally match them. It is specially noticeable the fact that LINC00570 and HOTTIP end up in the same community (whose according to Figure 2 in your paper should be separated). This is the code I have run:

seekr_download_gencode all -s human -r 37
seekr_canonical_gencode v37_all.fa v37_all_canonical.fa
seekr_norm_vectors v37_all_canonical.fa
seekr_kmer_counts v37_lncRNA_canonical.fa -o 6mers.csv -mv mean.npy -sv std.npy
seekr_pearson 6mers.csv 6mers.csv -o correlations_all_lncRNAs_kmers.csv
seekr_graph correlations_all_lncRNAs_kmers.csv 0.13 -g correlatons_communities.gml -c communities.csv -s 0 -n 5

Do you know why this is happening?? If you have any insight about this I would really appreciate it.

Thanks again for implementing SEEKR and for any help you might provide,

Best,
Kike