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Moderator: ATpoint

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ATpoint ♦ 40k
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Posts by ATpoint

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Comment: C: PCA on exon count data
... Yes, PCA is commonly performed on a set of informative (e.g. highly variable based on rowVar) genes based on the normalized and log2-transformed counts. The rowVar would also be performed on the norm/log counts of course. Nothing special with exon counts if you ask me. ...
written 6 hours ago by ATpoint ♦ 40k
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Comment: C: Bowtie2 > SAM > BAM > featureCounts - how to get into DESeq2(?)
... By the way, you use bowtie2, are you working with a non-splicing organism? bowtie2 is not splice-aware. Edit: Just saw your post from a couple of days ago, you are a microbiologist apparently, so no need for a splice-aware aligner apparently, never mind then. Can you share the command line of your ...
written 16 hours ago by ATpoint ♦ 40k
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Answer: A: Bowtie2 > SAM > BAM > featureCounts - how to get into DESeq2(?)
... The following is valid if you use the command line version of featureCounts, not the one from Rsubread. Assuming you ran something like `featureCounts -a your.gtf -o raw_featurecounts.txt *.bam` I recommend not changing anything in the output file. You can do all that in R. Assuming you have the ra ...
written 16 hours ago by ATpoint ♦ 40k
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Answer: A: extracting count matrix from default cell ranger files
... Non-programatical does not exist afaik. Follow the cellranger manual: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices library(Matrix) matrix_dir = "/opt/sample345/outs/filtered_feature_bc_matrix/" barcode.path <- paste0(matrix_d ...
written 19 hours ago by ATpoint ♦ 40k
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Comment: C: scaling difference between prcomp() and pcatools
... The error means that there is a column with all values being the same. Look, your code is a bit...unorganized, why don't you define `counts_norm_vst` on top, then subset to a common set of genes and then feed this matrix to both methods, turning off any feature selection in PCAtools to have things c ...
written 19 hours ago by ATpoint ♦ 40k
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Comment: C: scaling difference between prcomp() and pcatools
... `dds_vst_prc <- prcomp(counts_norm_vst, scale = TRUE)` Is `counts_norm_vst` transposed here? `mat_.1` seems to be, is the inconsistency based on missing transposition? ...
written 20 hours ago by ATpoint ♦ 40k
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Comment: C: What is the best peakcaller for H3 antibody?
... Maybe you could do ChIP on a couple of loci followed by qPCR and then show (as % against input) that in your treatment condition you get consistently less signal as this is an absolute measure against the input rather than sequencing which is relative (thinking aloud, https://www.biostars.org/u/401 ...
written 21 hours ago by ATpoint ♦ 40k
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Comment: C: What is the best peakcaller for H3 antibody?
... As I said, sequencing is typically not appropriate when you want to explore global changes because it is a relative measure. If everything changes, then relatively it looks the same. I personally would find WB the most convincing experiment while ChIP-seq would imho be inappropriate and a waste of m ...
written 21 hours ago by ATpoint ♦ 40k
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Comment: C: What is the best peakcaller for H3 antibody?
... Global decrease is also not measurable by ChIP-seq as you simply get lower amounts if precipitated DNA which is not a reliable measureI think. A WB definitively would be easier here and good to quantity protein amounts. ...
written 1 day ago by ATpoint ♦ 40k
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Comment: C: how to convert a big fasta file into several smaller one
... Hello yaqinguo629! Questions similar to yours can already be found at: how to convert a long fasta-file into many separate single fasta sequences We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in ...
written 1 day ago by ATpoint ♦ 40k

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Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 2 days ago, created an answer that has been accepted. For A: Get sequence by genomic coordinates in R
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Scholar 11 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Popular Question 12 days ago, created a question with more than 1,000 views. For Signal-to-Noise Plots for NGS Data; Selection of Background Regions
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Scholar 18 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
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Teacher 22 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
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Appreciated 24 days ago, created a post with more than 5 votes. For A: Get sequence by genomic coordinates in R
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Scholar 27 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
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