Moderator: Charles Warden

gravatar for Charles Warden
Charles Warden4.8k
Reputation:
4,800
Status:
Trusted
Location:
Duarte, CA
Website:
https://sites.google.c...
Twitter:
@cwarden45
Scholar ID:
Google Scholar Page
Last seen:
3 days, 14 hours ago
Joined:
4 years ago
Email:
c********@gmail.com

I am a Bioinformatics Specialist at City of Hope, where I work in the Integrative Genomics Core doing microarray and high-throughput sequencing analysis.

Posts by Charles Warden

<prev • 606 results • page 1 of 61 • next >
0
votes
2
answers
5.9k
views
2
answers
Comment: C: What is a typical workflow to correlate methylation and expression data?
... Lowering the delta-beta cutoff will only help if the methylated thresholds are also changed. You could try setting both methyl.cutoff and unmethyl.cutoff equal to 0.3, or disable the use of methylated thresholds by setting unmethyl.cutoff=1 and methyl.cutoff=0. Yes - in terms of posting etiquette, ...
written 15 days ago by Charles Warden4.8k
0
votes
1
answer
162
views
1
answers
Answer: A: How can we find the 16S rRNA sequence of an organism from NCBI?
... In most cases, it is difficult to confidently resolve classifications for 16S data at the species or sub-species level. So, if you were specifically interested in types of *Staphylococcus aureus*, it might be best to use a different marker (which you could define from comparing whole genome sequenc ...
written 25 days ago by Charles Warden4.8k
0
votes
2
answers
137
views
2
answers
Answer: A: convert BUSCO gff files to SNAP HMMs
... While I haven't directly used assemblage, I've done some testing with [MAKER][1], where I tended to get better results if I used protein / EST sequences (or an RNA-Seq *de novo* assembly) rather than starting with *de novo* gene predictions. Since it looks like assemblage is a modification of the M ...
written 6 weeks ago by Charles Warden4.8k
1
vote
1
answer
117
views
1
answers
Answer: A: Help for resource: Estimating age from 450k DNA methylation data
... The R code that you are supposed to run is within the Word / PDF files, which call the other files under "R Tutorials" At the beginning of the extracted R code, you'll need to define `dat0` as the beta matrix (such as `dat0 = read.table("probe_beta.txt",head=T, sep="\t")`) Also, at least with the ...
written 7 weeks ago by Charles Warden4.8k
0
votes
2
answers
204
views
2
answers
Comment: C: differential exon usage
... [DEXSeq][1] uses a specialized scripts (**dexseq_prepare_annotation.py** and **dexseq_count.py**) to run HTSeq for exon counts. The manual mentions that you can use other read counting programs, but I would typically use those specifically designed for DEXSeq (using a GTF annotation file). Juncti ...
written 7 weeks ago by Charles Warden4.8k
1
vote
2
answers
204
views
2
answers
Answer: A: differential exon usage
... If you are looking at differential exon usage (for patient characteristics, tumor-normal, etc.), DEXSeq is a popular option. I happen to like [JunctionSeq][1] (which is based upon DEXSeq), which also includes splice sites (known junctions, and novel junctions between known exons) and an overall p-v ...
written 7 weeks ago by Charles Warden4.8k
0
votes
1
answer
119
views
1
answers
Answer: A: Is there any reason not to run RS_ReadsOfInsert?
... Depends upon the library size - I believe the default setting is 3 cycles, and using 5 or 10 cycles is a little better if defining CCS reads. However, I typically don't see CCS reads greater than a few kb in length. For genome assemblies, especially if you have 10+ kb segments of repetitive elemen ...
written 7 weeks ago by Charles Warden4.8k
2
votes
1
answer
160
views
1
answers
Answer: A: Why Different naming for this 450k CpG in IlluminaHumanMethylation450kanno.ilmn1
... The probe name indicates the methylation context, which can be either CpG or CpH (or a SNP probe with an rsID). For example, ch.9.7776528F has hg19 coordinate chr9:7786528. The probe is for a CpH on the forward strand, so that position is a "C" and the next nucleotide is an "A" (H=A, C, or T). In ...
written 3 months ago by Charles Warden4.8k
0
votes
1
answer
185
views
1
answers
Answer: A: Error correcting PacBio reads prior to alignment with bwa mem
... I would say it is OK to use CCS reads, where it might be a good idea to impose 5x or 10x cutoffs (the default is 3x). I'm not as certain about error-corrected subreads if the library size is too large to define CCS reads. I guess it should be OK, but I can't really provide you with evidence from 1 ...
written 3 months ago by Charles Warden4.8k
2
votes
4
answers
4.8k
views
4
answers
Answer: A: Peak Detection In Intergenic Regions In Rna-Seq Data
... If you are trying to find deferentially expressed regions that don't necessarily match annotated regions, I would recommend [derfinder][1]. It's pretty quick (at least compared to trying to perform a novel assembly with cufflinks), although I typically would at least start by focusing on annotatio ...
written 4 months ago by Charles Warden4.8k

Latest awards to Charles Warden

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: Your Favorite Bioinformatics Blog(S) (2013 Edition)
Great Question 5 weeks ago, created a question with more than 5,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Memory Allocation for VarScan
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Your Favorite Bioinformatics Blog(S) (2013 Edition)
Scholar 3 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 4 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Student 5 months ago, asked a question with at least 3 up-votes. For Gatk Error: Samfilereader Appears To Be Using The Wrong Encoding For Quality Scores
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Popular Question 6 months ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
Scholar 9 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 11 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 533 users visited in the last hour