Moderator: Asaf

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Asaf3.7k
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Posts by Asaf

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Answer: A: Functional annotation from assembled contigs
... You need the assembly for prodigal. However, there are tools that run blastx against a database and these tools can use raw reads ...
written 21 hours ago by Asaf3.7k
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Comment: C: Starch Biosynthesis Pathway Reconstruction in Cassava using comparative and func
... See this post https://www.biostars.org/p/225812/ ...
written 1 day ago by Asaf3.7k
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Comment: C: Structure based phylogenic tree
... The key is finding a distance function between two genomes. Enjoy your HW. ...
written 2 days ago by Asaf3.7k
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Answer: A: fraction of genes up- and down-regulated
... 1. If might be a normalization effect meaning that some of the genes you see as upregulated didn't change while some of the genes you see as unchanged were actually downregulated. 2. You should account for the initial and final expression levels to compute total number of transcripts so it might b ...
written 2 days ago by Asaf3.7k
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Comment: C: Bioinformatics for food science
... You might want to listen to some episodes of taking biotech podcast by Kevin Folta. You'll get some ideas about what are the applications in the field and how bioinformatics relates to them. Look for episodes on molecular breeding, CRISPR/cas9. ...
written 2 days ago by Asaf3.7k
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Comment: C: Functional annotation from assembled contigs
... I wouldn't recommend to raise mink. I still suggest to run spades ...
written 3 days ago by Asaf3.7k
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Comment: C: Starch Biosynthesis Pathway Reconstruction in Cassava using comparative and func
... To answer your questions should take an entire semester, or the new biostars e-book :) ...
written 3 days ago by Asaf3.7k
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Comment: C: Functional annotation from assembled contigs
... It's pretty low... An average protein is 1000 bp long so half of the assembly will contain fragmented proteins. You can check the number of N's in the sequence itself, you can also compare N50 of the contigs to the scaffolds. You can try and assemble with metaSPAdes 3.9.0, it should give better res ...
written 3 days ago by Asaf3.7k
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Comment: C: Functional annotation from assembled contigs
... You can check how many N's you actually have in your data. I don't think it really matters for annotation (you'll get partial proteins anyway). For binning scaffolds might be more useful though. ...
written 3 days ago by Asaf3.7k
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Answer: A: Functional annotation from assembled contigs
... 1. use scaffold.fa make sure it's the last one created 2. you can start with prodigal for protein prediction, maybe others will have suggestions 3. You can map the reads (your input) against the scaffolds using bwa, bowtie2 etc. ...
written 3 days ago by Asaf3.7k

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