Moderator: Charles Warden

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Charles Warden4.6k
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Duarte, CA
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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

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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 20 days ago by Charles Warden4.6k
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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 5 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 6 weeks ago by Charles Warden4.6k
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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 3 months ago by Charles Warden4.6k

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
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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
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Teacher 16 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 16 months ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Teacher 19 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 19 months ago, created an answer with at least 3 up-votes. For A: Finding New Cancer Biomarket/Drug Target From Ngs Analysis
Scholar 19 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 19 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?
Scholar 21 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

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