User: Ryan Thompson

gravatar for Ryan Thompson
Ryan Thompson3.4k
Reputation:
3,380
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Trusted
Location:
TSRI, La Jolla, CA
Website:
https://github.com/Dar...
Twitter:
DarwinAwdWinner
Last seen:
4 months, 4 weeks ago
Joined:
8 years, 9 months ago
Email:
r**********@thompsonclan.org

I am a graduate student at The Scripps Research Institute. I analyze lots of deep sequencing data.

Posts by Ryan Thompson

<prev • 200 results • page 1 of 20 • next >
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Comment: C: Weird 1kb-periodic artifact in ChIP-Seq data (including input)
... I'm running `findMaxima` with range=5000 and `profileSites` with range=10000. ...
written 2.3 years ago by Ryan Thompson3.4k
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Comment: C: Weird 1kb-periodic artifact in ChIP-Seq data (including input)
... The reads were counted as the 5-prime ends of 147-bp fragments (i.e. the length of 1 nucleosome worth of DNA). ...
written 2.3 years ago by Ryan Thompson3.4k
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Comment: C: Weird 1kb-periodic artifact in ChIP-Seq data (including input)
... These are single-end reads. ...
written 2.3 years ago by Ryan Thompson3.4k
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Weird 1kb-periodic artifact in ChIP-Seq data (including input)
... I am doing a ChIP-Seq analysis of this [GEO data set](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73212). I was the data analyst on the original publication for that data set, which was done on hg19. I have now re-aligned the samples to hg38, and I'm using the csaw Bioconductor package to ...
chip-seq written 2.3 years ago by Ryan Thompson3.4k
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Comment: C: Best aligner for reporting all exact matches of multi-mapping short reads?
... What if I (by which I mean my collaborators) also want to map directly to a database of mature miRNA sequences instead of mapping to the genome? I expect the same options to mostly work, but the one case I'd worry about is when a read is longer than an annotated mature miRNA sequence by one or 2 bas ...
written 2.6 years ago by Ryan Thompson3.4k
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Comment: C: Best aligner for reporting all exact matches of multi-mapping short reads?
... This worked great! Thanks for the suggestion. ...
written 2.7 years ago by Ryan Thompson3.4k
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Comment: C: Best aligner for reporting all exact matches of multi-mapping short reads?
... This seems like a good option. Maybe you should convert this comment to an answer? ...
written 2.7 years ago by Ryan Thompson3.4k
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Best aligner for reporting all exact matches of multi-mapping short reads?
... I have about 30 GB (gzipped fastq) of small RNA (miRNA, etc.) sequencing data that I've been asked to align to the human genome (hg38), reporting for each read *every* position in the genome where it matches exactly. Bowtie2 has been my go-to mapper for short reads in the past, so I put together a p ...
bowtie2 speed alignment mirna written 2.7 years ago by Ryan Thompson3.4k
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Answer: A: TPM for ChIP-seq normalization
... If you have large differences in ChIP efficiency between samples, then you simply cannot detect global changes in binding, since these will be indistinguishable from efficiency bias. There is no normalization that can get around this problem. You would need to show using a separate data set that you ...
written 2.7 years ago by Ryan Thompson3.4k
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Is there a tool to convert soft clipping to hard clipping in bam files?
... My lab is developing a pipeline to analyze some paired-end methyl-seq data. One of the steps is to soft-clip overlaps between read pairs to prevent downstream tools from double-counting the overlapped region, using bamutil clipOverlap (http://genome.sph.umich.edu/wiki/BamUtil:_clipOverlap). However, ...
clipping bam written 2.7 years ago by Ryan Thompson3.4k

Latest awards to Ryan Thompson

Great Question 17 months ago, created a question with more than 5,000 views. For Gene-Level Analysis Of Rna-Seq Matched Pairs Of Samples?
Popular Question 17 months ago, created a question with more than 1,000 views. For Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formula?
Great Question 17 months ago, created a question with more than 5,000 views. For Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formula?
Popular Question 17 months ago, created a question with more than 1,000 views. For Is there a tool to convert soft clipping to hard clipping in bam files?
Popular Question 17 months ago, created a question with more than 1,000 views. For What Coordinate System Does Biomart Use?
Appreciated 17 months ago, created a post with more than 5 votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Popular Question 17 months ago, created a question with more than 1,000 views. For Best aligner for reporting all exact matches of multi-mapping short reads?
Great Question 17 months ago, created a question with more than 5,000 views. For What'S The Best Way To View And Explore A Large Gene Ontology Dag?
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Processing Fastq Files In R/Bioconductor Without Reading Entire Files Into Memory?
Great Question 2.2 years ago, created a question with more than 5,000 views. For Gene-Level Analysis Of Rna-Seq Matched Pairs Of Samples?
Epic Question 2.2 years ago, created a question with more than 10,000 views. For What'S The Best Way To View And Explore A Large Gene Ontology Dag?
Great Question 2.2 years ago, created a question with more than 5,000 views. For Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formula?
Great Question 2.2 years ago, created a question with more than 5,000 views. For Processing Fastq Files In R/Bioconductor Without Reading Entire Files Into Memory?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Computing Relative Coordinates Of One Bioconductor Granges Object To Another?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formula?
Great Question 2.2 years ago, created a question with more than 5,000 views. For What'S The Best Way To View And Explore A Large Gene Ontology Dag?
Student 2.2 years ago, asked a question with at least 3 up-votes. For Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
Good Question 2.5 years ago, asked a question that was upvoted at least 5 times. For Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
Prophet 2.5 years ago, created a post with more than 20 followers. For How Do I Do Simple Go Term Lookup Given A Gene (Or Mrna) Identifier?
Great Question 2.5 years ago, created a question with more than 5,000 views. For What'S The Best Way To View And Explore A Large Gene Ontology Dag?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Modeling Chip-Seq Background Using Edger'S Glm Functionality?
Good Question 2.7 years ago, asked a question that was upvoted at least 5 times. For Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Is Biostar Killing The Bioinformatics Core?

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