User: mamillerpa

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mamillerpa20
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Posts by mamillerpa

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Other genes that could account for my RNAseq reads?
... OK, thanks. A colleague at Penn also said that starting over with new mapping and counting may be the best choice. I haven't tried kallisto, but maybe this is just the motivation I need. But even if that is fast, I have found running the raw FASTQ through trimmomatic slow. (I think there's a lot ...
written 4 weeks ago by mamillerpa20
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Answer: A: JBrowse (and Tablet) only show Ensembl transcripts/can't search by gene ID or sy
... In JBrowse, I had to specify the attributes that I wanted when importing the GFF3 annotations bin/flatfile-to-json.pl -gff Mus_musculus.GRCm38.74.gff3 \ --trackType CanvasFeatures --trackLabel MmEns74_features \ --nameAttributes "name,id,ID,geneID,gene_name" ...
written 4 weeks ago by mamillerpa20
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JBrowse (and Tablet) only show Ensembl transcripts/can't search by gene ID or symbol
... I have deployed a JBrowse site, following http://jbrowse.org/code/JBrowse-1.14.1/docs/tutorial/ It's based on Ensembl 74 mouse. I'm pretty happy with how it's coming along, but **I can't seem to see the Ensembl genes, or search with gene IDs or gene symbols.** I do see, and can search on transcri ...
ensembl jbrowse tablet written 4 weeks ago by mamillerpa20
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Other genes that could account for my RNAseq reads?
... I have been asked to do differential and pathway analysis on some mouse RNAseq data. I was provided with FASTQs, BAMs, and gene/transcript report tables from rsem. The reads are 150 nt, paired-end from a MiSeq. rsem was run against GRCm38 with Ensembl 74 annotations. I'd like to reuse as much of ...
rna-seq written 4 weeks ago by mamillerpa20 • updated 4 weeks ago by h.mon15k
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Comment: C: Metagenomics with non-overlapping pairs
... thanks, I'll try AMPtk next week ...
written 6 months ago by mamillerpa20
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Metagenomics with non-overlapping pairs
... I've been doing metagenomics analyses for two collaborators over the past several months. The samples come from a variety of agricultural sources, but all are 250 nt paired end reads from MiSeq instruments. I have been doing the analyses with a combination of Qiime 1, Qiime2 and Phyloseq. The Qii ...
metagenomics non-overlapping pairs rna-seq written 6 months ago by mamillerpa20
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Comment: C: 1000 genomes frequencies from Ensembl SQL?
... Sorry about that, Emily. Am I supposed to withdraw one of the questions now? I just looked at the BioStars guidelines and do see a request for no crossposting. I don't see it on the Ensembl dev list guidelines page you linked. ...
written 23 months ago by mamillerpa20
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1000 genomes frequencies from Ensembl SQL?
... How would I write an SQL query to retrieve all of the frequencies, form all providers, such as seen on a page like http://useast.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=16:89919209-89920209;v=rs1805007;vdb=variation;vf=1232953 ? Connection info: http://useast.ensembl.org/info/data ...
ensembl sql 1000 genomes written 23 months ago by mamillerpa20
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Comment: C: How to get GO terms for E. Coli genes in R?
... Thanks, oganm. mart = useMart('ensembl') ; > listDatasets(mart) doesn't show anything for E. coli.  I was under the impression that Ensembl Bacterial didn't have a mart.     ...
written 4.0 years ago by mamillerpa20
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Comment: C: How to get GO terms for E. Coli genes in R?
... I have just parsed the "b numbers" and gene symbols out of the Ensmebl GFF file.  Then I can get symbol:GO term mappings from topGO Does this look even remotely reasonable? EcExpGFF <- read.delim("Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.22.gff3", header=FALSE, stringsAsFactors=F ...
written 4.0 years ago by mamillerpa20

Latest awards to mamillerpa

Scholar 4 weeks ago, created an answer that has been accepted. For A: JBrowse (and Tablet) only show Ensembl transcripts/can't search by gene ID or sy
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How to get GO terms for E. Coli genes in R?

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