User: Charles Warden

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

However, the feedback that I provide represent my own personal opinions.

Posts by Charles Warden

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Comment: C: VCF file from DanteLabs Dante Labs does not load in IGV

... Hi - I probably won't be ordering a Dante Labs kit this year. I'm trying to wrap up the analysis that of what I've submitted so far. Maybe next year :) I personally probably won't be using your data for analysis, but I think that is helpful. For example, this pre-print discussion indicated one v ...

written 16 hours ago by Charles Warden ♦ 7.0k

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Answer: A: Merge phased files from ShapeIT

... If your downstream program (like RFMix) also processes each chromosome separately, perhaps you want to wait on the merging step. I might have had other reasons to want to use a custom script to parse / join / filter .vcf files, but perhaps you could give [vcftools][1] a try? [1]: https://vcftoo ...

written 3 days ago by Charles Warden ♦ 7.0k

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Comment: C: Is it possible to directly convert fastq to CRAM ?

... Thank you for pointing out the .fastq versus .fastq.gz discussion. .cram functionality is kind of important for both reads (which you are discussing) as well as alignment (since I believe there are programs that don't accept .cram as an input). However, the feedback about the reference being impor ...

written 4 days ago by Charles Warden ♦ 7.0k

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Answer: A: Is it possible to directly convert fastq to CRAM ?

... While some programs require uncompressed .fastq files, many/most will accept .fastq.gz files. Creating **.fastq.gz** files will considerably save space for long-term storage. I'm not sure how this compares to CRAM, but it has considerable storage savings with greater functionality (since very few ...

written 5 days ago by Charles Warden ♦ 7.0k

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Comment: C: Using Varscan without a matched normal

... I think you will need to have several rounds of analysis and discussion for your projects. So, having exposure to a certain amount of ideas is important, but you also need first-hand experience to be confident in your results. In other words, if you think something is worth trying, then you should ...

written 5 days ago by Charles Warden ♦ 7.0k

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Comment: C: Biological replicates and depth seq

... Hi Morris. I would use an independently calculated FPKM expression value for quality control plots and assessing differential expression strategies (as long as you have replicates, I would preferably test out at least [DESeq2][1] / [limma-voom][2] / and [edgeR][3] for every project). Even though I ...

written 5 days ago by Charles Warden ♦ 7.0k

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Comment: C: insert figure and code in the post of Biostars?

... I think this should arguably be the "accepted" answer - I have used this tutorial several times: https://www.biostars.org/p/309884/#346552 However, "thank you" everybody for your contributions :) ...

written 6 days ago by Charles Warden ♦ 7.0k

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Answer: A: Biological replicates and depth seq

... I would usually expect more noise among genes with lower expression. However, I think it matters **i)** what is the total number of aligned reads per sample and **ii)** what is the variation between samples. In other words, if your samples are low coverage, perhaps I understand a large difference ...

written 6 days ago by Charles Warden ♦ 7.0k

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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?

... Hi - I edited your response to show the alignment in the plot (I had to right-click on the image to open just the image in another window, and then provide that slightly different hyperlink. I'm not sure how big a deal the green reads are, but it looks like the proportion of green reads is less tha ...

written 6 days ago by Charles Warden ♦ 7.0k

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Comment: C: Too many differentially expressed genes in RNA-seq?

... Yes - I strongly agree with having a fold-change filter. While it is a slightly different topic, I thought this was an issue when the number of differentially expressed genes was approaching the number of genes in the genome (which would lead to inappropriate power calculations): https://disqus.com ...

written 7 days ago by Charles Warden ♦ 7.0k

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Teacher 4 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

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