User: rrcutler

gravatar for rrcutler
rrcutler110
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110
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Location:
United States
Last seen:
11 months, 2 weeks ago
Joined:
3 years, 3 months 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 14 months ago by rrcutler110
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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 14 months ago by rrcutler110
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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 14 months ago by rrcutler110
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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 2.1 years ago by rrcutler110
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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 2.1 years ago by rrcutler110 • updated 2.1 years ago by Rob2.6k
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Comment: C: Combine multiple query results in blastn
... Meant blastn, thanks for catching that. ...
written 2.1 years ago by rrcutler110
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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 2.1 years ago by rrcutler110 • updated 2.1 years ago by Prasad1.5k
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Comment: C: Mauve Similarity plots - similar or not?
... Thanks a lot for the clarification! ...
written 2.1 years ago by rrcutler110
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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 2.1 years ago by rrcutler110
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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 2.2 years ago by rrcutler110

Latest awards to rrcutler

Popular Question 12 months 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
Student 2.1 years ago, asked a question with at least 3 up-votes. For Does TPM account for fragments?

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