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urol-e5 / molecular-prelim

Exploring test data sets to see how to best determine states
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Capture lyijin/spis_dna_meth coverage files into our workflows #2

Open sr320 opened 4 years ago

sr320 commented 4 years ago

https://zenodo.org/record/1211456#.XnuLjJNKisp

sr320 commented 4 years ago

more urls https://advances.sciencemag.org/content/4/6/eaar8028
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA386774
https://zenodo.org/record/1211456#.XnuLVZNKimk
https://github.com/lyijin/spis_dna_meth/

sr320 commented 4 years ago

added files to repo

sr320 commented 4 years ago

Next will inspect and see if can integrate into our bs workflow..

sr320 commented 4 years ago

problem: cannot find genome with same scaffold naming.

Spis.scaffold1|size2969787  9571    9571    88.8888888888889    16  2   SpisGene1   0.27284 2436    -6494   Intron_3_-10    0.69829 570 -247
Spis.scaffold1|size2969787  9695    9695    95.4545454545455    21  1   SpisGene1   0.28673 2560    -6370   Intron_3_-10    0.85006 694 -123
Spis.scaffold1|size2969787  9696    9696    88.8888888888889    16  2   SpisGene1   0.28684 2561    -6369   Intron_3_-10    0.85129 695 -122
Spis.scaffold1|size2969787  9826    9826    94.4444444444444    17  1   SpisGene1   0.3014  2691    -6239   Exon_4_-10  0.07328 8   -108
Spis.scaffold1|size2969787  9827    9827    100 11  0   SpisGene1   0.30151 2692    -6238   Exon_4_-10  0.0819  9   -107
>NW_019217784.1 Stylophora pistillata isol
hputnam commented 4 years ago

is it this one? http://spis.reefgenomics.org/

sr320 commented 4 years ago

Yep that looks better than what I found on NCBI!