Moderator: Charles Warden

gravatar for Charles Warden
Charles Warden4.6k
Reputation:
4,570
Status:
Trusted
Location:
Duarte, CA
Website:
https://sites.google.c...
Twitter:
@cwarden45
Scholar ID:
Google Scholar Page
Last seen:
4 days, 3 hours ago
Joined:
3 years, 7 months 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 • 596 results • page 1 of 60 • next >
0
votes
2
answers
197
views
2
answers
Comment: C: BWA-MEM using long PacBio reads
... Last time I checked, the acceptable output formats depended upon the input format - for example, I remember the change to not allow direct .sam file creation if the input is a .bam file. However, I have a version of BLASR installed in this [Docker image][1] that will at least work with the followin ...
written 8 days ago by Charles Warden4.6k
2
votes
2
answers
637
views
2
answers
Comment: C: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
... Actually, this is not correct: the example given for single-end data on the RSeQC website may be a little confusing because it is the opposite of what you typically observe in Illumina stranded libraries (but there is a verbal description of what the strand code represent). The counts are for reads ...
written 10 days ago by Charles Warden4.6k
0
votes
2
answers
197
views
2
answers
Answer: A: BWA-MEM using long PacBio reads
... BWA is OK to use with CCS reads (preferably with at least 5 or 10 cycles), but that .fastq file seems quite large (and, unfortunately, unless you get a more raw data format, you can't use PacBio functions to define CCS reads). You could also use BLASR with a .fasta file, but the recommendation is t ...
written 11 days ago by Charles Warden4.6k
0
votes
4
answers
2.8k
views
4
answers
Comment: C: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... CIBERSORT is designed for immune cell types. If you aren't specifically looking a mixture of immune cells, you might want to use a more generalized deconvolution strategy. If you are looking at bulk tumor expression, I would typically expect some sort of percent tumor value from the pathologist, w ...
written 11 days ago by Charles Warden4.6k
2
votes
6
answers
238
views
6
answers
Answer: A: HISAT2 or Tophat2
... I would say it depends on what you want to do with your data. I've sometimes found that the TopHat alignments work better than STAR alignments with some splicing analysis programs, possibly due to the format of the alignment. I would consider the run-time for TopHat to be sufficiently quick that y ...
written 13 days ago by Charles Warden4.6k
0
votes
1
answer
107
views
1
answers
Answer: A: RNA-SeQC does not calculate information about "Strand Specificity"
... You can see https://www.biostars.org/p/125344/ for more information about getting strand-specific information from RSeQC via infer_experiment.py. I'm not familiar with the report format that you provided, but I know that `infer_experiment.py` works. You can also double-check that chromosome format ...
written 13 days ago by Charles Warden4.6k
0
votes
2
answers
179
views
2
answers
Answer: A: How can I count one specific exon in RNA-seq data
... [DEXSeq][1] is a good suggestion. If you wanted to use [JunctionSeq][2] for splicing analysis, [QoRTs][3] can provide exon and splice junction counts. [1]: http://www.bioconductor.org/packages/2.10/bioc/html/DEXSeq.html [2]: https://bioconductor.org/packages/release/bioc/html/JunctionSeq.html ...
written 14 days ago by Charles Warden4.6k
1
vote
4
answers
194
views
4
answers
Answer: A: 16S rRNA seq software
... For differential abundance, you can use [metagenomeSeq][1]. You may also get similar results using limma for abundance/frequency or limma-voom for counts. mothur also has a related [metastats][2] function, as well as a random forest classification function in [classify.rf][3]. If you are using Il ...
written 14 days ago by Charles Warden4.6k
0
votes
1
answer
154
views
1
answers
Answer: A: JunctionSeq: using continuous covariates, is it possible?
... Unless you want to start altering the JunctionSeq code, I don't believe they've added the ability analyze continuous covariates. For exon coverage, you could use DEXSeq. Or, if you use the QoRTs counts for JunctionSeq, you could analyze the exon and junction counts separately (so, junctions get a ...
written 10 weeks ago by Charles Warden4.6k
0
votes
2
answers
175
views
2
answers
Answer: A: find cancer related methylation in lncRNA though online database
... If you really mean "in" lncRNAs (as in RNA methylation), then that may be a little harder to collect than nearby or overlapping DNA methylation. That said, it looks like there is at least one database for m6A modifications (for mammals): http://compgenomics.utsa.edu/methylation/ --> [MeT-DB P ...
written 11 weeks ago by Charles Warden4.6k

Latest awards to Charles Warden

Student 26 days 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 26 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
Teacher 5 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 5 weeks ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
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
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 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
Scholar 6 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 7 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 7 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
Scholar 10 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 15 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 15 months ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Popular Question 17 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Finding New Cancer Biomarket/Drug Target From Ngs Analysis
Teacher 17 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 18 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
Scholar 18 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
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Scholar 20 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
Popular Question 20 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Popular Question 20 months ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Finding New Cancer Biomarket/Drug Target From Ngs Analysis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1058 users visited in the last hour