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User: igor

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igor • 4.3k
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Posts by igor

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Comment: C: What is contained in the GRCh38 reference, and how was it constructed?
... Keep it mind that the original reference human genome was completed in 2003. Many people have been working on improving it ever since, so it's a lot of work. ...
written 23 hours ago by igor • 4.3k
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Comment: C: How detrimental are duplicate reads in RNAseq experiments?
... Good find. However, the paper mostly discusses single-cell RNA-seq. Regarding normal bulk RNA-seq, they say: > In the Illumina labs, the team also experimented with purposefully > generating a large number of PCR duplicates. The team compared data > from unique reads and duplicates—'good' ...
written 23 hours ago by igor • 4.3k
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Comment: C: FASTQ to SAM File converter
... Definitely faster than some of those fancy aligners. ...
written 14 days ago by igor • 4.3k
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Comment: C: overlap BED files, but account for region name
... Thanks for confirming. I just wanted to make sure I am not reinventing the wheel or missing something. ...
written 14 days ago by igor • 4.3k
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Comment: C: FASTQ to SAM File converter
... You should figure out exactly what you are trying to do and understand the whole process before trying to find "the fastest tools". ...
written 14 days ago by igor • 4.3k
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overlap BED files, but account for region name
... I recently found ReMap which is a great resource of TF binding sites across different studies. They [provide][1] the binding sites in BED format where each region is named based on the TF. Although it's relatively trivial to overlap two BED files (using something like `bedtools fisher` or `bedtools ...
overlap bed bedtools written 14 days ago by igor • 4.3k • updated 14 days ago by Chris Miller ♦ 18k
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Answer: A: Deseq2 pairwise comparision
... Did you check the DESeq2 vignette? There is a section on paired samples: > Yes, you should use a multi-factor design which includes the sample > information as a term in the design formula. This will account for > differences between the samples while estimating the effect due to the > ...
written 20 days ago by igor • 4.3k
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Answer: A: How to normalize 450K data for cell type composition
... This is very delayed, but it seems there is another package `celltypes450` that can adjust beta values for cell-type composition: https://github.com/brentp/celltypes450 It was originally created before `estimateCellCounts` was available. Perhaps there is a good reason why `estimateCellCounts` doesn ...
written 23 days ago by igor • 4.3k
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Answer: A: Chromatin Accessibility Data and RNA-seq
... A paper just came out that addresses that question: [Modeling gene regulation from paired expression and chromatin accessibility data][1]. Hopefully that is not what inspired your question. [1]: http://www.pnas.org/content/early/2017/06/01/1704553114.abstract ...
written 23 days ago by igor • 4.3k
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Answer: A: Calculate Variant Allele Frequency in a TCGA dataset
... Yes, you're correct. VAF is `t_alt_count / (t_ref_count + t_alt_count)`. When dealing with allele frequencies, also be careful regarding the context. They can be referring to fraction of reads in a single sample (since you are dealing with cancer data, that is probably the case) or fraction of indi ...
written 23 days ago by igor • 4.3k

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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
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Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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