User: Malcolm.Cook

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Malcolm.Cook1.1k
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kansas, usa
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Posts by Malcolm.Cook

<prev • 143 results • page 1 of 15 • next >
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Answer: A: How Do I Overlay Tracks In Genomic Viewers Such As Igv Or Igb?
... Old question, new answer... it is now possible in IGV to overlay tracks based on having a common attribute. See "Tracks > Overlay Data Tracks". I use it often to overlay line-graphs of replicate data. It makes the variance "pop". ...
written 9 weeks ago by Malcolm.Cook1.1k
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Comment: C: Question: Pheatmap annotation
... glad you figured this out... I had the same problem... did not realize that the rownames of the column_annotations had to match with the colnames of the matrix.... I thought it was positional until I found this post. ...
written 10 weeks ago by Malcolm.Cook1.1k
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Comment: C: Retrieve coordinate for maximum value in a region using a bigwig file
... What if there are ties? ...
written 3 months ago by Malcolm.Cook1.1k
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Answer: A: Find overlapping blast hits and keep the highest evalue
... Here's an approach using R: The [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html) package provides function `disjoin` with which you can compute all disjoint (non-overlapping) ranges of your hits. When passed optional argument `with.revmap=TRUE`, the results ...
written 4 months ago by Malcolm.Cook1.1k
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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 months 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 months 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 5 months 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 5 months 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 5 months ago by Malcolm.Cook1.1k • updated 5 months ago by RamRS28k
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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 6 months ago by Malcolm.Cook1.1k

Latest awards to Malcolm.Cook

Teacher 17 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 18 months ago, received more than 100 upvotes.
Scholar 18 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 20 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Scholar 20 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 22 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 2.7 years ago, created 100 posts.
Teacher 2.7 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 3.7 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 4.5 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 5.3 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 5.7 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 6.2 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 6.3 years ago, voted at least 25 times.
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 6.3 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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