User: Alternative

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Alternative230
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Posts by Alternative

<prev • 39 results • page 1 of 4 • next >
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Detecting highly variable genes within replicates
... Hello, We are looking for a method to detect/extract genes that show variability within biological replicates (typically 3 replicates) of the same condition. Differential expression algorithms (DESeq2, EdgeR) will consider only genes (or group of genes) that show similarity in their expression pro ...
gene expression variability written 28 days ago by Alternative230 • updated 28 days ago by Michele Busby1.9k
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Answer: A: ATAC-seq: differential peaks using macs2 bdgdiff yields strange results
... Differential analysis depends on raw read counts. Macs2 generates very large and diffuse peaks for ATAC-seq and chromatin marks. As such, a differentially called peak may not be real since the difference is calculated between hundreds of reads for large peaks and when you check them visually, they w ...
written 8 months ago by Alternative230
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Comment: C: Remove batch effect from exome data
... Yes, I just run some: Duplication is very high but expected since we have targeted sequencing. Additionally, since samples correspond to PPFE, I checked in my VCFs the count of C > T conversions expected to be enriched for such samples. There, I found that the 2 over-mutated batches are the one ...
written 17 months ago by Alternative230
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Remove batch effect from exome data
... Dear all, We run targeted exome sequencing for ~100 samples divided in 6 sequencing batches. We noticed a batch effect whereby the samples coming from 2 of the 6 batches are heavily mutated. All samples were sequenced using the same protocol. Any idea on how to remove batch effect from exome seque ...
exome exome sequencing ngs batch effect batch written 17 months ago by Alternative230
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Comment: A: Powerful desktop computer for genomics
... Many thanks all for your replies. Very helpful. ...
written 2.8 years ago by Alternative230
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Powerful desktop computer for genomics
... Dear all, I would like to purchase a desktop computer to be used by a student to run NGS pipelines for whole genome exome sequencing, RNA-seq, ChIP-seq and other similar applications. No need for Whole Genome Sequencing nor assembly pipelines. Which desktop computer exists in the market and able t ...
next-gen chip-seq rna-seq sequencing written 2.8 years ago by Alternative230
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Comment: C: Doubts related to MACS tool
... sorry for the late reply. Here are the answers regarding the different points: 1) yes, it is supposed to be done separately. When you call peaks with the SPMR option, MACS will generate two bedgraph files (that you can convert to the better bigwig format), one for your treatment and one for your inp ...
written 3.0 years ago by Alternative230
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Comment: C: Does MNase increase Multi mapper fraction?
... What do you mean by multimappers. - Are those reads that map to multiple locations in the genome ? - What are you performing the ChIP on. Is it a protein that binds on low complexity/repetitive/duplicated regions ? - What is your duplication rate (many reads mapping exactly at the same location o ...
written 3.3 years ago by Alternative230
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Answer: A: Doubts related to MACS tool
... There are two different things: "Sample normalization" and "Noise deduction". 1) you can normalize any library you sequenced by Reads Per Million. This is what the SPMR is for. When this option is specified, you will have that done on your "treatment" and "Control". You can then transform both to " ...
written 3.3 years ago by Alternative230
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Answer: A: Log2 fold change heatmap
... For me, it doesn't make sense. You will be duplicating the information in the heatmap with two columns showing the same information.   ...
written 3.3 years ago by Alternative230

Latest awards to Alternative

Popular Question 16 months ago, created a question with more than 1,000 views. For Powerful desktop computer for genomics
Scholar 23 months ago, created an answer that has been accepted. For A: Generate heatmap or table showing genes found in multiple tests
Scholar 3.6 years ago, created an answer that has been accepted. For A: Generate heatmap or table showing genes found in multiple tests

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