User: Michele Busby

gravatar for Michele Busby
Michele Busby1.8k
Reputation:
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Location:
United States
Website:
http://scotty.genetics...
Twitter:
michelebusby
Last seen:
11 hours ago
Joined:
5 years, 5 months 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 • 127 results • page 1 of 13 • next >
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Comment: C: DNA Hybridization Melting Temperature Open Source
... Thank you Pierre! That did the trick ...
written 1 day ago by Michele Busby1.8k
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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 2 days ago by Michele Busby1.8k • updated 2 days ago by Pierre Lindenbaum110k
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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 3 days ago by Michele Busby1.8k
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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 24 days ago by Michele Busby1.8k
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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 27 days ago by Michele Busby1.8k
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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 27 days ago by Michele Busby1.8k • updated 27 days ago by h.mon16k
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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 8 weeks ago by Michele Busby1.8k
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Answer: A: How to remove the RIN (RNA integrity number) effect for RNA-seq data?
... You may want to try looking at the supplements for the GTEx papers. They did a lot of work on that. It also depends a lot on the protocol. If it is PolyA selected you will get biases against short genes because you will lose the 5' end. If it is RNA depleted or hybrid capture your bias will be diffe ...
written 11 weeks ago by Michele Busby1.8k
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Answer: A: Can I add TPM values of Isoforms of the same gene to get total gene expression?
... If they are calculated correctly (e.g. with RSEM or similar), the quantification should be divided among the isoforms in a mutually exclusive way. So if you have Isoform1 3 TPM - three transcripts Isoform2 1 TPM - one transcript The total gene should have 4 transcripts per million (i.e. 4 inde ...
written 5 months ago by Michele Busby1.8k
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Answer: A: Sub-typing patients by a single gene's expression in TCGA dataset.
... Do I understand correctly that you are dividing the samples by the expression of the gene (rather than observing the expression of the gene in different groups)? If so, the first thing I would do is make a histogram of the log TPM and see if it is bimodal. Then if it is you will know where the cuto ...
written 5 months ago by Michele Busby1.8k

Latest awards to Michele Busby

Appreciated 16 days ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Appreciated 16 days ago, created a post with more than 5 votes. For A: Chip-Seq merging peak files
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 5 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Scholar 5 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Popular Question 10 months ago, created a question with more than 1,000 views. For Tool For Visualizing Sections Of Sequences
Commentator 15 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 16 months ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 18 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Centurion 18 months ago, created 100 posts.
Scholar 19 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Appreciated 2.1 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 2.1 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 2.5 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 3.2 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Guru 3.3 years ago, received more than 100 upvotes.
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 3.6 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 3.7 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Good Answer 3.9 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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