Moderator: Asaf

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Asaf4.7k
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Posts by Asaf

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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 5 days ago by Asaf4.7k
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Comment: C: How to highlight regions in RNA second structure
... 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 9 days ago by Asaf4.7k
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Answer: A: What genome assembler to choose for an unpaired FASTQ data derived from a Birch
... I'll go with SPAdes, try it with and without --meta ...
written 10 days ago by Asaf4.7k
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Comment: C: Error in my DESeq script
... It's called rubber-duck debugging. You take a rubber duck, put it next to your screen and explain to it what you did. Most of the time you'll catch the bug. Happy to be a rubber duck. For the next time, try to set up a start to end pipeline without human intervention, these types of errors can have ...
written 10 days ago by Asaf4.7k
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Comment: C: Error in my DESeq script
... You probably get NAs somewhere in the building process so var==var[1] is neither TRUE nor FALSE. Do you have NAs in the countData matrix? ...
written 10 days ago by Asaf4.7k
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Answer: A: Annotation with Prokka - small ORFs and genus-specific DB?
... some thoughts: 1. You can try and predict all ORFs with EMBOSS transeq for instance and look for domains using interproscan - you might find some putative short ORFs that way. 2. I guess by downloading assemblies of a lot of salmonella genomes and extracting the genes but in this case, since most ...
written 18 days ago by Asaf4.7k
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Comment: C: multiple DNA sequences aligned to the same gene
... It's three reads that were mapped to the same gene, to different positions along the gene (183-206, 175-200 and 178-206). Looks like your alignment is working as it should. ...
written 24 days ago by Asaf4.7k
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Comment: C: minION from oxford nanopore, is it still so promising?
... They had a real bump in accuracy after May 2016. In addition I only used 2D reads, the median quality was above Q20. It gave long contigs but they were still full of errors, usually in poly-nucleotides (i.e. is AAAAA, AAAA or AAAAAA?), combined with Illumina reads the assembly was really good. ...
written 25 days ago by Asaf4.7k
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Answer: A: minION from oxford nanopore, is it still so promising?
... We used it through an outsource service for bacterial genomes. The reads were better than I expected, combined with Illumina reads we got almost a whole chromosome. The problem with the system (as we saw it) is that the costs are a bit obscure, you can use the flow-cell several times but you should ...
written 25 days ago by Asaf4.7k
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Comment: C: converting paired end reads to single end, is this a good idea?
... If the only difference between the libraries is sequencing then you should be fine but I would just take read1 and ignore the other side, it might influence counting mapping to genes. However, I suspect that some other factors are different between these sets of libraries, e.g. fragmentation, select ...
written 25 days ago by Asaf4.7k

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