User: Malcolm.Cook

gravatar for Malcolm.Cook
Malcolm.Cook1.0k
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kansas, usa
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http://www.google.com/...
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1 day, 4 hours ago
Joined:
9 years, 1 month ago
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Posts by Malcolm.Cook

<prev • 129 results • page 1 of 13 • next >
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Comment: C: ensembl mysql servers and helpdesk non-responsive. Is it me?
... Indeed- we recently changed approach to spam management with a few headaches including lost emails. Thanks for you patience and excellent support! ...
written 1 day ago by Malcolm.Cook1.0k
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Answer: A: ensembl mysql servers and helpdesk non-responsive. Is it me?
... doh. my problem was that my ~/.my.cnf was providing a password ...
written 3 days ago by Malcolm.Cook1.0k
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ensembl mysql servers and helpdesk non-responsive. Is it me?
... While following the instructions for [Using Terminal to Connect to Ensembl public MySQL Servers](https://www.biostars.org/p/270746/) my connections are being rejected, viz: ~$ mysql -h useastdb.ensembl.org -u anonymous -P 5306 ERROR 1045 (28000): Access denied for user 'anonymous'@'ip-10-51 ...
ensembl mysql written 3 days ago by Malcolm.Cook1.0k • updated 3 days ago by Emily_Ensembl18k
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Answer: A: Identify reads that span intron-exon junctions in RNA-Seq
... I have used `featureCounts` function from the [Rsubread](https://bioconductor.org/packages/release/bioc/html/Rsubread.html) package for this express purpose and found it worked perfectly. I recommend it if you work in `R` because: + it gives you precise control over the extent of overlap you wan ...
written 11 weeks ago by Malcolm.Cook1.0k
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Comment: C: 5', 3' SS and Intron retention read count using STAR out.tab
... No: based on my reading of the paper and skimming the source code, it appears to me that SGSeq does not analyze IR. ...
written 12 weeks ago by Malcolm.Cook1.0k
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Comment: C: How to extract filename and change text in the same file
... Sure. In general, in your command line: - `{}` gets replaced with the file being processed. - `{=perl expression=}` gets replaced with the value of a perl expression being evaluated in the context of the perl variable `$_` being set to the name of the file being processed. So, in my example, ...
written 3 months ago by Malcolm.Cook1.0k
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Comment: C: How to extract filename and change text in the same file
... thanks for the fix and the alternate! ...
written 3 months ago by Malcolm.Cook1.0k
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Answer: A: How to extract filename and change text in the same file
... If you have GNU parallel installed, you can use it instead of a bash for loop: parallel 'sed -i "s|Sample1$|{=s/.new.vcf$//=}|"' {} ::: *.new.vcf ...
written 3 months ago by Malcolm.Cook1.0k
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Answer: A: How to subset reads from fastq file to use as test file on a script
... I believe the answer remains seqtk - c.f. https://www.biostars.org/p/6544/#42695 ...
written 4 months ago by Malcolm.Cook1.0k
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Answer: A: Is there a standard file format for anchored contigs?
... [ALLMAPS: robust scaffold ordering based on multiple maps](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0573-1) (github: [ALLMAPS](https://github.com/tanghaibao/jcvi/wiki/ALLMAPS)) project documentation includes [ALLMAPS: How to use different types of genomic maps](https://git ...
written 5 months ago by Malcolm.Cook1.0k

Latest awards to Malcolm.Cook

Teacher 3 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 4 months ago, received more than 100 upvotes.
Scholar 4 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 6 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Scholar 6 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 8 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 19 months ago, created 100 posts.
Teacher 19 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
Scholar 2.5 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 3.4 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 4.5 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 5.0 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 5.2 years ago, voted at least 25 times.
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 5.2 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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