User: mamillerpa

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mamillerpa30
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Posts by mamillerpa

<prev • 13 results • page 1 of 2 • next >
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Comment: C: which genes have altered transcript proportions?
... So far I have only tried RATS, but it's clearly more sophisticated than anything I could have thrown together. It's also faster than what I described above, but it still takes several minutes on a modern Windows laptop. I haven't looked into multi-threading for tximport or RATS yet. I also need t ...
written 27 days ago by mamillerpa30
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which genes have altered transcript proportions?
... I collected some rsem isoforms.results files and created a data frame with the transcript ID, the isoform percentage, and an experimental condition (mutant or wildtype) > head(one.var, n=8) transcript_id IsoPct GENO.COHORT 3246628 ENSMUST00000000028 62.32 MUTANT ...
star rsem rna-seq written 27 days ago by mamillerpa30 • updated 27 days ago by h.mon19k
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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 months ago by mamillerpa30
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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 months ago by mamillerpa30
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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 months ago by mamillerpa30
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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 months ago by mamillerpa30 • updated 4 months ago by h.mon19k
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Comment: C: Metagenomics with non-overlapping pairs
... thanks, I'll try AMPtk next week ...
written 9 months ago by mamillerpa30
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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 9 months ago by mamillerpa30
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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 2.2 years ago by mamillerpa30
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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 2.2 years ago by mamillerpa30

Latest awards to mamillerpa

Scholar 4 months 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 4.2 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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