Moderator: Asaf
Asaf ♦ 5.0k
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Posts by Asaf
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... Hi all,
I'm working on mouse gut microbiome samples and want to use kraken to get their taxonomic profile. I'm using kraken2 with the databases nt and bacteria (plus some others).
The problem is that there are bacterial sequences integrated in some genomes in nt, they can be easy to track like weird ...
written 9 weeks ago by
Asaf ♦ 5.0k
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444
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Comment:
C: Adapter Removal - Nextera LIbrary
... You can use cutadapt with multiple -a and -A flags ...
written 5 months ago by
Asaf ♦ 5.0k
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536
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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 10 months ago by
Asaf ♦ 5.0k
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351
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... I think you can BLAST them against nr and see where they came from, you should get 100% identity ...
written 10 months ago by
Asaf ♦ 5.0k
3
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... I think it's now integrated into spades, use -plasmid flag ...
written 10 months ago by
Asaf ♦ 5.0k
0
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1
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779
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1
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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 10 months ago by
Asaf ♦ 5.0k
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639
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... I think you're missing a new-line at the end of the GTF file ...
written 10 months ago by
Asaf ♦ 5.0k
0
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1
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779
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1
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Comment:
C: Mothur alignment issues
... Your query sequence is 213k long? ...
written 10 months ago by
Asaf ♦ 5.0k
0
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1
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729
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1
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... What is the assembly quality? Why do you need scaffolds? ...
written 10 months ago by
Asaf ♦ 5.0k
0
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350
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1
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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 11 months ago by
Asaf ♦ 5.0k
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