User: rrcutler

gravatar for rrcutler
rrcutler120
Reputation:
120
Status:
Trusted
Location:
United States
Last seen:
7 months, 1 week ago
Joined:
4 years, 5 months ago
Email:
r*******@email.wm.edu

Posts by rrcutler

<prev • 24 results • page 1 of 3 • next >
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Access edgeR test statistic
... I'd like to know an easy way to access test statistics calculated after using the exactTest() function in edgeR. I'd like to use these with fdrtool to attempt to estimate corrected FDR values due to a skewed p-value distribution. Currently, in the object produced by this function, I can only access: ...
edger written 7 months ago by rrcutler120 • updated 7 months ago by Gordon Smyth1.1k
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Comment: C: Running multiple read-pairs with Trinity on Galaxy
... I'll try this, thanks. ...
written 2.4 years ago by rrcutler120
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Comment: C: Running multiple read-pairs with Trinity on Galaxy
... Okay, that is reasonable. I was not aware of the other site. I got directed to post a question on this site when using galaxy from the tab: Help -> Ask a question ...
written 2.4 years ago by rrcutler120
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(Closed) Running multiple read-pairs with Trinity on Galaxy
... Hello fellow Galaxy users, I am trying to use Trinity to assemble NGS reads from 9 samples that each have paired-end reads. However, I am unable to load multiple Left and Right reads so that all 18 of the fastq files can be run together. I see that input can be of 3 types: single dataset, multiple ...
assembly rna-seq written 2.4 years ago by rrcutler120
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IGV popup on alignment track
... Hello all, I blasted an assembly to a reference and then displayed the alignments in IGV. When I hover over each alignment I get a set of metrics which I cannot seem to find any documentation for. Any clarification on what XE, RG, NM, and AS is? Also What is the Cigar metric and how is the duplicat ...
igv written 3.3 years ago by rrcutler120
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Does TPM account for fragments?
... Hello all, I understand the differences between RPKM, which normalizes for read depth and then gene length; FPKM, the same thing as RPKM but does not count reads twice if both came from the same fragment; and TPM which normalizes for gene length, then read length - allowing comparison of read count ...
rna-seq written 3.3 years ago by rrcutler120 • updated 3.3 years ago by Rob3.6k
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Comment: C: Combine multiple query results in blastn
... Meant blastn, thanks for catching that. ...
written 3.3 years ago by rrcutler120
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Combine multiple query results in blastn
... Hello all, This may be already answered, but I could not find anything addressing this particular question. I am blasting contigs of a de novo genome assembly against the data base to determine which organism is most similar. However, in the blast results, I get metrics of how similar each separate ...
blastn written 3.3 years ago by rrcutler120 • updated 3.3 years ago by Prasad1.6k
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Comment: C: Mauve Similarity plots - similar or not?
... Thanks a lot for the clarification! ...
written 3.3 years ago by rrcutler120
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Comment: C: Increasing kmer limit in SPAdes
... Thanks for the clarification. Looking at kmer coverage I have a kmer coverage of 166 ...
written 3.3 years ago by rrcutler120

Latest awards to rrcutler

Supporter 7 months ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Gene symbol to mRNA sequence (refseq.rna)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For MPprimes vs. PCRTiler for PCR Multiplexing
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Increasing kmer limit in SPAdes
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Gene symbol to mRNA sequence (refseq.rna)
Popular Question 3.2 years ago, created a question with more than 1,000 views. For MPprimes vs. PCRTiler for PCR Multiplexing
Student 3.2 years ago, asked a question with at least 3 up-votes. For Does TPM account for fragments?

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