User: grp2009
grp2009 • 20
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Posts by grp2009
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... I didn't realize it when I posted the question, but Bandage has a command line mode, including a command `querypaths` that accomplishes precisely the task in question.
First, find out where the Bandage executable lives. On a Mac, you select the Bandage application, do "Show Package Contents", and t ...
written 17 days ago by
grp2009 • 20
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... Briefly, I am trying to automate the process of aligning a query sequence (from FASTA) to an assembly graph (FASTG from Spades assembly). As output I need the sequences of the paths in the assembly graph corresponding to the alignment(s).
More detail: I have used Spades to assemble the genome from ...
written 22 days ago by
grp2009 • 20
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... Are there any papers that study these issues (rRNA level as surrogate for RNA degradation, etc.)? ...
written 6 months ago by
grp2009 • 20
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... > 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 16 months ago by
grp2009 • 20
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... 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 17 months ago by
grp2009 • 20
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... So far I have not found anything interesting that can be done with these genes, but I haven't kept looking. ...
written 17 months ago by
grp2009 • 20
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... 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 ...
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... 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 ...
written 2.5 years ago by
grp2009 • 20
• updated
2.5 years ago by
Vijay Lakhujani ♦ 4.1k
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... 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 ...
written 2.8 years ago by
grp2009 • 20
Latest awards to grp2009
Scholar
17 days ago,
created an answer that has been accepted.
For A: Alignment to fastg assembly graph
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