User: Malcolm.Cook

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Malcolm.Cook1.1k
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Posts by Malcolm.Cook

<prev • 139 results • page 1 of 14 • next >
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Comment: C: Edited Title: Finding differential sequence characteristics between two groups o
... Hi. Not sure I can help further. If you are able to fully respond to my original "Answer" to your question, I might have some ideas for you. ...
written 5 weeks ago by Malcolm.Cook1.1k
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Comment: C: How to rename multiple fastq files
... Hi @Ole - I thought the Q() would allow the recipe to work even if filename had whitespace in them but I guess that was unneeded over-protection... yes? ...
written 5 weeks ago by Malcolm.Cook1.1k
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Comment: C: Edited Title: Finding differential sequence characteristics between two groups o
... Well, my comment/guess intends to better elicit from you what your actual *problem* is. I read the answers provided so far, and felt they *might* be aimed at answering a different question than you have. With a clearer *problem* statement, I, or others, might make a more informed stab at a *soluti ...
written 6 weeks ago by Malcolm.Cook1.1k
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Answer: C: sequence similarity analysis between groups of closely related DNA sequences
... From your description, my *guess* is that you want to characterize which *kind of* modifications (M) result in your original unmodified sequence (US) to be assigned the same experimental group (USG) as their modified counterparts (MS) experimentally assigned group (MSG). If so, it would help to kno ...
written 6 weeks ago by Malcolm.Cook1.1k
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Answer: A: How to rename multiple fastq files
... [GNU Parallel](https://www.gnu.org/software/parallel/) lets you harness the power of perl regular expressions: parallel --dry-run mv {=Q($_)=} {=Q(s/GEN\d+_N_(\w+)_lib\d+_\d+_(\d+_R\d)/$1_$2/)=} ::: *.fastq note: run it once with the `--dry-run` to make sure it does what you want, then run aga ...
written 6 weeks ago by Malcolm.Cook1.1k • updated 5 weeks ago by RamRS26k
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... This discussion is primarily about the interplay of normalization and visualization in the context of the tool csaw which I am now using for ATAC-seq and find quite performant and flexible and all-in-one I recommend you read the paper & manual. ...
written 10 weeks ago by Malcolm.Cook1.1k
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... `normOffsetsNQ` as written above actually normalizes the **log** of cpm (per the `log=TRUE` on the `edgeR::cpm` call). It then computes the offsets and converts them back into "natural base". In this I am following the advice of one of the author of csaw, Aaron Lun, private communication. I am in ...
written 10 weeks ago by Malcolm.Cook1.1k
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Answer: A: ATAC-seq sample normalization (quantil normalization)
... If you want to use quantile normalization with csaw, try this: library(preprocessCore) # which implements normalize.quantiles normOffsetsNQ<- function (object, ..., assay.id = "counts") { mat <- assay(object, i = assay.id, withDimnames = FALSE) mat.cpm <- edgeR:: ...
written 10 weeks ago by Malcolm.Cook1.1k
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Comment: C: Difference in the percentage of reads falling into intronic and coding regions
... Differences in library preparation that effect fraction of DNA retained. Ideally none. We're they both poly-a selected? Difference in intron retention between the samples. I highly doubt this, but mention it as a possibility. Were all the 10 samples in batch 2 somehow consistently different from ...
written 7 months ago by Malcolm.Cook1.1k
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Comment: C: Extract only RNA-seq reads in a BAM file that extend into an intron
... If you were you able to do this, can you advise what you plan on doing next? I ask because if you next intend to tabulate *how many* reads extend into each end of each intron, then you might profitably skip extracting them and directly count them through creative use of RSubread's [FeatureCounts: ...
written 8 months ago by Malcolm.Cook1.1k

Latest awards to Malcolm.Cook

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequ
Guru 13 months ago, received more than 100 upvotes.
Scholar 14 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 15 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Scholar 16 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequ
Centurion 2.4 years ago, created 100 posts.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequ
Scholar 3.3 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 4.1 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 5.3 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 5.8 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 6.0 years ago, voted at least 25 times.
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequ

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