User: Hansen_869

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Hansen_86920
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Posts by Hansen_869

<prev • 49 results • page 1 of 5 • next >
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Protein/peptide characterization/properties tools
... Hi, For my research project, I need to compare the outputs of different protein analysis tools. I will be using known proteins (such as HGH), and I want to discover whether or not these tools provide me with the same results (for the same analysis). What I'm looking for is tools that can predict p ...
properties protein characterization peptide written 5 weeks ago by Hansen_86920 • updated 5 weeks ago by genomax92k
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Comment: C: comparative gene quantification, problem with COGs and hypothetical proteins.
... I see. I just don't get, how a single copy marker gene is identified, if Musicc is just given a KO/COG ID and an abundance number. ...
written 9 months ago by Hansen_86920
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Comment: C: comparative gene quantification, problem with COGs and hypothetical proteins.
... I see. I just don't get, how a single copy marker gene is identified, if Musicc is just given a KO/COG ID and an abundance number. ...
written 9 months ago by Hansen_86920
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Comment: C: comparative gene quantification, problem with COGs and hypothetical proteins.
... But do I have to associate my genes with KO? I'm not familar with KO. You wrote a list of KO-IDs, are those the same as the single-copy proteins? ...
written 9 months ago by Hansen_86920
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Comment: C: comparative gene quantification, problem with COGs and hypothetical proteins.
... Cool thanks! After examing the reference and if I understand it correctly: I provide an abundance file of the genes and their mapped reads to Musicc, and then I can confidently assign them to COGs? Also, do I have to TPM normalize afterwards? ...
written 9 months ago by Hansen_86920
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comparative gene quantification, problem with COGs and hypothetical proteins.
... I have 8 metagenomic samples (bacterial DNA) that I have generated count-matrixes for (I used Prokka for annotation). This means, that I now have the abundance of all genes, in all of my 8 samples. I have then normalized my samples with TPM (Transcript per Million reads), as my sample sizes are of d ...
gene tpm cog abundance written 9 months ago by Hansen_86920
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Comment: C: Accounting for differences in FASTQ-file size, when comparing metagenomic gene a
... Thanks for your response. I will look into that. Do you suggest i do any other form of normalisation? I read about TPM, RPKM and FPKM. Or do you think normalising for JUST gene length is sufficient in this type of study? In the mentioned techniques, READ length is taken into account, but due to the ...
written 10 months ago by Hansen_86920
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Accounting for differences in FASTQ-file size, when comparing metagenomic gene abundance between samples
... I have 8 count-matrix's (from bacterial metagenomic DNA sequencing), with information regarding fragment-count, meaning number of fragments aligned to each gene. I got the fragment-count, as opposed to read count, using Featurecounts. I have normalized for gene-length (longer genes will map more re ...
gene reads metagenomics tpm written 10 months ago by Hansen_86920 • updated 10 months ago by tshtatland60
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Comment: C: Mapping to contigs or predicted genes, for quantitative gene analysis (DNAseq)
... Ah yes, that's what it is! I have 8 big samples to compare. The goal is to look at the difference in gene/cog abundance between the samples. How do you suggest i approach that, in regards to normalization (and comparison, any tools)? (Writing this comment from a friends user, due to comment limit. ...
written 12 months ago by Hansen_86920
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Comment: C: BWA index - is it neccesary?
... So I shouldn't feed my original fasta-file to BWA mem ? When I index my fasta file, the resulting fasta file is empty. I suppose something is wrong? ...
written 12 months ago by Hansen_86920

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