Moderator: Asaf
Asaf ♦ 4.8k
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Posts by Asaf
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... I don't think you need to select at all. Are your sRNAs from human or bacteria? If from bacteria then they should be long (up to ~150 nt) ...
written 9 weeks ago by
Asaf ♦ 4.8k
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... I think you can BLAST them against nr and see where they came from, you should get 100% identity ...
written 11 weeks ago by
Asaf ♦ 4.8k
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... I think it's now integrated into spades, use -plasmid flag ...
written 12 weeks ago by
Asaf ♦ 4.8k
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338
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Comment:
C: Mothur alignment issues
... OK, you have 213k sequences which is fine.
Can you print the command line you used? ...
written 12 weeks ago by
Asaf ♦ 4.8k
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... I think you're missing a new-line at the end of the GTF file ...
written 12 weeks ago by
Asaf ♦ 4.8k
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Comment:
C: Mothur alignment issues
... Your query sequence is 213k long? ...
written 12 weeks ago by
Asaf ♦ 4.8k
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281
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... What is the assembly quality? Why do you need scaffolds? ...
written 12 weeks ago by
Asaf ♦ 4.8k
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148
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... From my limited knowledge in NNs I think that you shouldn't represent 3D structures using features. The great benefit of NNs is that the machine can generate features. I think that you would want to have the angles between AAs as input and the AAs themselves so you'll have 20+ dimension vector. You ...
written 3 months ago by
Asaf ♦ 4.8k
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... I did it some long time ago with Vienna package. They have a script to paint RNA structure according to some measure, I changed the script to read custom input. ...
written 3 months ago by
Asaf ♦ 4.8k
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... I'll go with SPAdes, try it with and without --meta ...
written 3 months ago by
Asaf ♦ 4.8k
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