User: Matthew Thornton

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300
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USA, Los Angeles, USC
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Posts by Matthew Thornton

<prev • 32 results • page 1 of 4 • next >
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Comment: C: What are the methods to get count data per cell from single cell fastq given onl
... Thank you very much for your explanation. I would have to install CellRanger on a large multipurpose (academic) linux cluster. I was hoping to avoid this, as I have STAR installed already. I will give scPipe a try. I will probably also use Cell Ranger locally. ...
written 3 days ago by Matthew Thornton300
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Comment: C: What are the methods to get count data per cell from single cell fastq given onl
... I will do that. Thank you!! ...
written 3 days ago by Matthew Thornton300
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What are the methods to get count data per cell from single cell fastq given only R1, R2, and I1 fastq files
... Hello, I am starting to process single cell RNA sequencing data and I noticed that all of the bioconductor tutorials for single cell (https://f1000research.com/articles/5-2122/v2) start from well groomed data that is already in a count matrix with cells for columns and genes for rows . This is pret ...
single cell fastq written 14 days ago by Matthew Thornton300 • updated 12 days ago by Gordon Smyth36k
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Comment: C: DEXSeqHTML and biomart object
... Ok so this looks like the answer to my question, sorry I didn't see it first.  I am confused, how do you know for sure that the 'ensembl_gene_id' lines up with the 'ensembl_gene_id' in dxr?  I guess because you pull from it  initially with values=geneIDs(dxd)?  Thanks!! ...
written 11 months ago by Matthew Thornton300
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Comment: C: Annotation of DEXSeqHTML with biomaRt
... Could you post as an answer how you would add annotations using DEXSeqHTML?  I would be nice to have more, info, like the descriptions, but I would settle for just the external_gene_names. Could it be that there is not enough room in HTML table? ...
written 11 months ago by Matthew Thornton300
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Comment: C: Annotation of DEXSeqHTML with biomaRt
... I will try this. Can a vector be used with the attributes switch with DEXSeqHTML? Thank you! ...
written 11 months ago by Matthew Thornton300
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Annotation of DEXSeqHTML with biomaRt
... Hello!  I am trying to annotate the output of DEXSeqHTML for ease of my collaborators.  I am using the code but not getting any annotation. Does anyone else have this problem? DEXSeqHTML(dxr1, genes=NULL, path="DEXSeqReport", file="testForDEU.html", fitExpToVar="condition", FDR=0.1, color=NULL, co ...
biomart dexseq written 11 months ago by Matthew Thornton300
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Figuring out what long decent Phred value unaligned reads are
... Hello! My question is about reads that don't align to the genome yet are long and have very good Phred scores. Currently, my workflow is FastQC > Cutadapt > Trimmomatic > RNA-STAR > HTSeq-count > edgeR (RUVSeq) I use gencode genomes with Ensembl IDs and even with the cleanest isolati ...
rnaseq alignment written 2.4 years ago by Matthew Thornton300
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xps - error in normalize - "Error: Length of non-varying units is zero."
... Hello! I am trying to optimize my data processing with xps. I am getting an error when using the normalize function. It could be due to improper switches. here is the error: > data_norm <- normalize(data_bkgrd, "Normalize_Step2", filedir=outdir, tmpdir="", update = FALSE, select = "pmonly", ...
normalization process xps written 4.7 years ago by Matthew Thornton300 • updated 4.7 years ago by cstrato3.9k
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Comment: C: External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
... Thank you for the suggestions! I will look at where the ERCC controls fall in the data. I am thinking to use a paired-down set of the ERCC controls in the 'linear' range and which are within my experimental data. I am planning to use the spike-in probes procedure in the vsn package. I will also try ...
written 4.7 years ago by Matthew Thornton300

Latest awards to Matthew Thornton

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Importing RMA processed data into limma for eBayes
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Popular Question 2.4 years ago, created a question with more than 1,000 views. For What is the easiest way to make the GC content and length matrix for package cqn?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Limma design and contrast matrix question.

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