Moderator: Charles Warden

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Charles Warden6.4k
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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.

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

Posts by Charles Warden

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Comment: C: Finding the best model for expression data (RNA-Seq counts)
... Yes - I believe the rlog is mostly similar to log2(FPKM+0.1) values. So, it is more like the log2-transformed values (rather than the linear values that need a rounding factor prior to a log-transformation). There are some examples of the comparisons between rlog and log2(counts/CPM + X) values he ...
written 1 hour ago by Charles Warden6.4k
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Comment: C: ASEReadCounter More then one variant context at position
... I'm not entirely sure about the cause of that error message, but it is admittedly usually best to work with the data type from which an algorithm was developed (I believe I've tested those allele counters with TopHat2 and STAR, but not with BWA-MEM or Bowtie2). So, I think at least one of those wou ...
written 2 hours ago by Charles Warden6.4k
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Answer: A: ASEReadCounter More then one variant context at position
... I'm not sure what extra complications you might encounter with ATAC-Seq data versus RNA-Seq data. However, I have the following suggestions: **1)** Last time I checked, I thought the GATK ASEReadCounter only worked for SNPs. If you are already throwing out all indels, then only focusing on unambi ...
written 2 days ago by Charles Warden6.4k
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Comment: C: problem for 2 different normalization methods in train and test data set
... Hi, I can't really promise any method will be the best option ahead of time - I would expect some troubleshooting / benchmarking to be necessary for each project. The best option that I can think of is to split the TCGA up into training and validation datasets (or, really validation set #1 and val ...
written 3 days ago by Charles Warden6.4k
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Answer: A: problem for 2 different normalization methods in train and test data set
... I can think of at least two possibilities: **1)** Request access to controlled access TCGA data. I think higher impact papers often do some re-processing of that raw data. You might still have batch effects between library types that can't completely be corrected, but you can run a program like [ ...
written 3 days ago by Charles Warden6.4k
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Comment: C: All CpG sites in human genome RRBS
... I agree that RRBS coverage will vary (but I think the number of shared sites at 10X coverage is a useful QC metric). So, even if you find the conclusions are a little different for your own experiment, perhaps it is worth taking a look at this [Carmona et al. 2017](https://www.ncbi.nlm.nih.gov/pubm ...
written 4 days ago by Charles Warden6.4k
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Answer: A: Running STAR aligner with paired-end and single-end reads simultaneously
... I typically use single-end 50 bp reads for gene expression analysis. If you are just interested in getting counts for differential expression (and FPKM/CPM for visualization), perhaps trim the longer R1 from the PE experiment to 75 bp? To be safe, I probably would start by processing them separate ...
written 4 days ago by Charles Warden6.4k
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Comment: C: Hardware requirement for RNA-seq
... I would typically run TopHat2 with 8 GB of RAM and 4 cores on a cluster (and I ran STAR with similar run time a few times, even though I think it tends to use more RAM when run on a computer that has extra RAM available). However, that is with [50 bp Single-End reads][1]: if you have paired-end rea ...
written 4 days ago by Charles Warden6.4k
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Comment: C: Finding the best model for expression data (RNA-Seq counts)
... Also, as requested, I will move this to an answer (and edit the beginning to be a little less confusing). ...
written 4 days ago by Charles Warden6.4k
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Comment: C: Finding the best model for expression data (RNA-Seq counts)
... You are welcome. While I technically have the ability to edit your post, you really should be doing that instead of me. At the bottom of the grey box (near "add reply"), there is an `edit` button. You can also add a note at the end if you wanted to make clear you changed it due to a response from ...
written 4 days ago by Charles Warden6.4k

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