User: rrcutler

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rrcutler100
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United States
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8 months, 1 week ago
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3 years ago
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r*******@email.wm.edu

Posts by rrcutler

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Running multiple read-pairs with Trinity on Galaxy
... I'll try this, thanks. ...
written 11 months ago by rrcutler100
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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 11 months ago by rrcutler100
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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 11 months ago by rrcutler100
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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 22 months ago by rrcutler100
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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 22 months ago by rrcutler100 • updated 22 months ago by Rob2.3k
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Comment: C: Combine multiple query results in blastn
... Meant blastn, thanks for catching that. ...
written 22 months ago by rrcutler100
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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 22 months ago by rrcutler100 • updated 22 months ago by Prasad1.5k
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Comment: C: Mauve Similarity plots - similar or not?
... Thanks a lot for the clarification! ...
written 22 months ago by rrcutler100
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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 22 months ago by rrcutler100
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Comment: C: Hisat2 versus Bowtie2
... I got similar results of bowtie2 mapping better (97.42%) than Hisat2 (93.74%) when mapping raw reads (unfiltered) to assembled contigs. Which should I trust more, since it seems Hisat2 can't use a local alignment, as Devon said. ...
written 23 months ago by rrcutler100

Latest awards to rrcutler

Popular Question 8 months ago, created a question with more than 1,000 views. For Gene symbol to mRNA sequence (refseq.rna)
Popular Question 21 months ago, created a question with more than 1,000 views. For MPprimes vs. PCRTiler for PCR Multiplexing
Student 21 months ago, asked a question with at least 3 up-votes. For Does TPM account for fragments?

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