User: Michele Busby

gravatar for Michele Busby
Michele Busby1.9k
Reputation:
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Location:
United States
Website:
http://scotty.genetics...
Twitter:
michelebusby
Last seen:
1 day, 8 hours ago
Joined:
6 years, 1 month ago
Email:
b************@gmail.com

Computational biologist at an oncology startup, formerly at the Broad Institute. I developed Scotty application for performing RNA Seq power analysis while completing my PhD in Gabor Marth's lab.

Posts by Michele Busby

<prev • 130 results • page 1 of 13 • next >
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Comment: C: Detecting highly variable genes within replicates
... I don't think you need to assume a normal distribution but I haven't looked at the theory in a while. The main thing is that you can add uncorrelated variances to get the total variance. They are probably something like a lognormal distribution but the tail is constrained by biology so you can usual ...
written 12 days ago by Michele Busby1.9k
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Answer: A: Detecting highly variable genes within replicates
... This is a good question and you were wise to ask it because I don't think the obvious approach is the correct one. For RNA Seq, the observed variance that you get from calculating the variance in the replicates will have a mixture of biological + technical variance. If the libraries are good, the ...
written 22 days ago by Michele Busby1.9k
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Answer: A: HLA Typing understanding
... I am not sure at what level you are confused, so forgive me if this is too basic. This is an explainer on how the HLAs are named: http://hla.alleles.org/nomenclature/naming.html Functionally, you only care about the first few digits. HLA-A - this is the gene. There are a bunch of HLA genes. HL ...
written 6 months ago by Michele Busby1.9k
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Comment: C: DNA Hybridization Melting Temperature Open Source
... Thank you Pierre! That did the trick ...
written 8 months ago by Michele Busby1.9k
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DNA Hybridization Melting Temperature Open Source
... Hi, Is there a good open source software for calculating the melting temperature of two DNA sequences? I have been trying the Biopython MeltingTemp module but it relies on tables for the possible mismatches and many of the possible mismatches are not in the tables, so my sequences get kicked out. ...
sequence written 8 months ago by Michele Busby1.9k • updated 8 months ago by Pierre Lindenbaum117k
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Answer: A: Statistical test for replicates
... When you sequence small RNA you often get reads that are the degradation products of longer mRNA. These might be what you are seeing. It will be better or worse depending on the protocol. If it is just a size selection there will be a lot of junk. If you are looking for miRNA there is an enzyme that ...
written 8 months ago by Michele Busby1.9k
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Answer: A: fastq- dump error
... I got this today too and it actually proceeded through to the whole download even though it had the error message. So maybe wait and see if it finishes? You can do an "ls" to see if it's still loading. If it gives you the stats at the end it's good. ...
written 8 months ago by Michele Busby1.9k
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Answer: A: RSEM build for C. elegans
... I figured it out but I'll leave it here if anyone else runs into this: RSEM expects a ; after the transcript_id. It's not here in this version of the file. This adds the : to the line and seems to fix it: sed -i 's/$/;/' c_elegans.PRJNA13758.WS253.canonical_geneset.fixed.gtf ...
written 9 months ago by Michele Busby1.9k
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RSEM build for C. elegans
... Hi, Has anyone had luck getting an RSEM build for worm? I am using: rsem-prepare-reference --gtf /Worm/c_elegans.PRJNA13758.WS253.canonical_geneset.gtf \ --polyA-length 25 --polyA /Worm/c_elegans.PRJNA13758.WS253.genomic_softmasked.fa \ /Worm/c_elegans.PRJNA13758.WS253/RSEM/transc ...
rna-seq written 9 months ago by Michele Busby1.9k • updated 9 months ago by h.mon24k
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Answer: A: quantification RNAseq and normalization
... Hi KML, I think you need to step back for a moment and think about what each measurement is good for. In general, you want to use counts when you are looking at the expression of one gene in multiple conditions and TPM when you are comparing or ranking the expression of different genes. You start ...
written 10 months ago by Michele Busby1.9k

Latest awards to Michele Busby

Appreciated 8 months ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Appreciated 8 months ago, created a post with more than 5 votes. For A: Chip-Seq merging peak files
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 13 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Scholar 13 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Popular Question 18 months ago, created a question with more than 1,000 views. For Tool For Visualizing Sections Of Sequences
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 2.2 years ago, created an answer that has been accepted. For A: Coverage for sample with many species
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Centurion 2.2 years ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Coverage for sample with many species
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Guru 3.9 years ago, received more than 100 upvotes.
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 4.3 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design

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