User: grp2009

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grp200920
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Posts by grp2009

<prev • 10 results • page 1 of 1 • next >
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Comment: C: bcftools consensus failure
... The `-s` option of `bcftools consensus` is meant for specifying the sample name (i.e. if the input is a multi-sample VCF file, this tells bcftools which sample to pick). Can you see what the sample name is in the VCF file? ...
written 20 days ago by grp200920
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Answer: A: Alignment to fastg assembly graph
... 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 7 months ago by grp200920
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Alignment to fastg assembly graph
... 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 ...
assembly alignment written 7 months ago by grp200920
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Comment: C: rRNA removal needed for salmon / DESeq2 analysis
... Are there any papers that study these issues (rRNA level as surrogate for RNA degradation, etc.)? ...
written 13 months ago by grp200920
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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 23 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 24 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 24 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 24 months ago by grp200920 • updated 22 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 3.0 years ago by grp200920 • updated 3.0 years ago by lakhujanivijay4.6k
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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 3.4 years ago by grp200920

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Scholar 7 months ago, created an answer that has been accepted. For A: Alignment to fastg assembly graph

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