User: grp2009

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grp200920
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Posts by grp2009

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Answer: A: Are OTUs an accurate measure of abundance?
... > For example if we have OTU10 which has an OTU count of 2 and another OTU1 which has an OTU count of 1000 mean that only 2 bacterial cells of OTU10 are present in the environment It certainly does not mean that there are 2 bacterial cells belonging to OTU10 in the environment/sample. There is n ...
written 5 months ago by grp200920
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Comment: C: Ribosomal reads in shotgun metagenomics data
... From what I understand, `bbsplit` would allow me to map reads to reference genomes. In contrast, I'm talking about reads that do not map to any known reference genome. I would like to connect these unmapped reads (by overlapping/assembling) to the reads that mapped (imperfectly) to known ribosomal g ...
written 6 months ago by grp200920
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Comment: C: Immunoglobulins in RNA-seq results
... So far I have not found anything interesting that can be done with these genes, but I haven't kept looking. ...
written 6 months ago by grp200920
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Ribosomal reads in shotgun metagenomics data
... I am looking at some shotgun (not amplicon) metagenomics data, and have observed that among the reads that are classified as belonging to specific bacteria, most are from ribosomal genes (as determined later by BLAST). This is despite the fact that this is not targeted amplicon sequencing. My interp ...
microbiome metagenomics sequencing written 6 months ago by grp200920 • updated 4 months ago by Biostar ♦♦ 20
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Features that distinguish phyla in 16S sequences
... Is there a way to use RDP (Ribosomal Database Project) or a similar taxonomy classification tool to produce localized "features" that distinguish 16S sequences based on their phyla? By "feature" I mean something like a region of the 16S sequence that is particularly important in distinguishing betwe ...
next-gen sequencing written 18 months ago by grp200920 • updated 18 months ago by Vijay Lakhujani2.5k
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Immunoglobulins in RNA-seq results
... I am working with some RNA-seq results from mice - specifically, a comparison of infected and naive mice. Among the differentially expressed genes are numerous immunoglobulin variable regions - Igkv8-27, Ighv13-2, Igkv10-94, and so forth. Do these identifiers give me any useful information about th ...
sequence rna-seq written 23 months ago by grp200920

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