Moderator: Asaf

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Asaf5.0k
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Israel
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Posts by Asaf

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Kraken2 database curation
... 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 ...
metagenomics kraken written 10 days ago by Asaf5.0k
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Comment: C: Adapter Removal - Nextera LIbrary
... You can use cutadapt with multiple -a and -A flags ...
written 3 months ago by Asaf5.0k
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Comment: C: Suggestion on Improving mRNA and sRNA mapping
... 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 8 months ago by Asaf5.0k
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Answer: A: Assign taxonomy to protein fasta file
... I think you can BLAST them against nr and see where they came from, you should get 100% identity ...
written 8 months ago by Asaf5.0k
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Answer: C: Download link for plasmidSPAdes
... I think it's now integrated into spades, use -plasmid flag ...
written 8 months ago by Asaf5.0k
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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 8 months ago by Asaf5.0k
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Comment: C: Adding plasmid sequences to gtf file
... I think you're missing a new-line at the end of the GTF file ...
written 8 months ago by Asaf5.0k
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Comment: C: Mothur alignment issues
... Your query sequence is 213k long? ...
written 8 months ago by Asaf5.0k
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Comment: C: How to use SPADES assembler to de novo assembly contigs
... What is the assembly quality? Why do you need scaffolds? ...
written 8 months ago by Asaf5.0k
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Answer: A: Best Representation of Protein Sequences
... 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 9 months ago by Asaf5.0k

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Teacher 18 days ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Scholar 9 weeks ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Popular Question 6 months ago, created a question with more than 1,000 views. For Transcription Network With Edges Type
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Good Example Sequence For Psi-Blast
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Help With Nussinov'S Rna Folding Algorithm
Popular Question 8 months ago, created a question with more than 1,000 views. For Transcription Network With Edges Type
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
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Scholar 11 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
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