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 • 131 results • page 1 of 14 • next >
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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 6 weeks 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 12 weeks ago by Malcolm.Cook1.1k
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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 4 months ago by Malcolm.Cook1.1k
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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 4 months ago by Malcolm.Cook1.1k
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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 4 months ago by Malcolm.Cook1.1k • updated 4 months ago by Emily_Ensembl19k
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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 6 months ago by Malcolm.Cook1.1k
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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 7 months ago by Malcolm.Cook1.1k
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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 `$_` being set to the name of the file being processed. So, in my example, ...
written 7 months ago by Malcolm.Cook1.1k
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Comment: C: How to extract filename and change text in the same file
... thanks for the fix and the alternate! ...
written 7 months ago by Malcolm.Cook1.1k
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Answer: A: How to extract filename and change text in the same file
... If you have GNU parallel installed, you can use it instead of a bash for loop: parallel 'sed -i "s|Sample1$|{=s/.new.vcf$//=}|"' {} ::: *.new.vcf ...
written 7 months ago by Malcolm.Cook1.1k

Latest awards to Malcolm.Cook

Teacher 7 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 8 months ago, received more than 100 upvotes.
Scholar 8 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 10 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Scholar 11 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 12 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 23 months ago, created 100 posts.
Teacher 23 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 2.9 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 3.7 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 4.8 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
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: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 5.5 years ago, voted at least 25 times.
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 5.5 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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