User: mamillerpa

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mamillerpa30
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Posts by mamillerpa

<prev • 14 results • page 1 of 2 • next >
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extract gene subsequences that have supporting RNASeq evidence
... I'd like to report, as nucleotide sequences, the portions of some genes that are covered by RNAseq data. I've written the following, but it seems slow and awkward. I have a feeling I shouldn't have to convert form one kind of range to a dataframe and then to another kind of range, or convert the s ...
rna-seq written 27 days ago by mamillerpa30
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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 3 months 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 3 months ago by mamillerpa30 • updated 3 months ago by h.mon21k
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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 6 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 6 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 6 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 6 months ago by mamillerpa30 • updated 6 months ago by h.mon21k
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Comment: C: Metagenomics with non-overlapping pairs
... thanks, I'll try AMPtk next week ...
written 11 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 11 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 2.4 years ago by mamillerpa30

Latest awards to mamillerpa

Scholar 6 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 4.4 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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