User: Malcolm.Cook

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Malcolm.Cook970
Reputation:
970
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Location:
kansas, usa
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http://www.google.com/...
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Last seen:
3 days, 17 hours ago
Joined:
8 years, 10 months ago
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Posts by Malcolm.Cook

<prev • 121 results • page 1 of 13 • next >
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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 13 days ago by Malcolm.Cook970
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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 7 weeks ago by Malcolm.Cook970
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Comment: C: Automating to convert multiple fastq files into one fastq file
... Great - glad to help - please upvote and accept the answer! ...
written 10 weeks ago by Malcolm.Cook970
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Comment: C: Automating to convert multiple fastq files into one fastq file
... I can not help you much more than to say to install the latest version of Gnu parallel that is packaged for your operating system distribution. probably install with: sudo apt-get install parallel but best to follow you OS documentation, possibly such as: [Installing softwares](https://commun ...
written 11 weeks ago by Malcolm.Cook970
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Comment: C: Automating to convert multiple fastq files into one fastq file
... Sure. The approach is the same; you just need *two* calls to `cat`, using slightly different file wildcarding (aka [globbing](http://tldp.org/LDP/abs/html/globbingref.html)) in each. Also, I now realize your well identifier has a row and a column component. In this updated example, for brevity, I ...
written 12 weeks ago by Malcolm.Cook970
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Answer: A: Automating to convert multiple fastq files into one fastq file
... Install and use [GNU Parallel](https://www.gnu.org/software/parallel/). Then use the following model. Remove `--dry` when you're ready to run: nPlates=3 nWells=4 parallel -k --dry 'bwa aln -t 4 GMbwaidx <(cat NGS/*{1}_{2}*.fastq) > {1}_{2}.sam' :::: <( seq -f 'P%03g' ${nPlate ...
written 12 weeks ago by Malcolm.Cook970
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Comment: C: How can keep the change in my fastq file when i use grep and sed to edit it?
... re: "simply run the `sed` command" - note: you must pass `-i` to modify it in place (assuming GNU `sed`) ...
written 12 weeks ago by Malcolm.Cook970
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Answer: A: How can keep the change in my fastq file when i use grep and sed to edit it?
... I understand "keep the change in my fastq file " to mean precisely the opposite of "Leaving your original file unmodified", to wit: GNU `sed` provides the `-i` option to apply the edit in place sed -i '1~4s/^@/@ILLUMINA/' test.fastq Perl too, allowing perl -p -i -e 's/^@/@ILLUMINA/ unle ...
written 12 weeks ago by Malcolm.Cook970
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Answer: A: gene set enrichment analysis
... I've used both Broad's JAVA application and clusterProfiler's R implementation of [GSEA](https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/GSEA) and recommend it as performing the same analysis and producing near identical charts. Also, if you adopt it, there are a a bun ...
written 4 months ago by Malcolm.Cook970
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... even if they are on different strands? ...
written 4 months ago by Malcolm.Cook970

Latest awards to Malcolm.Cook

Guru 9 days ago, received more than 100 upvotes.
Scholar 13 days ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 9 weeks ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Scholar 12 weeks ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 4 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 14 months ago, created 100 posts.
Teacher 15 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 2.2 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 3.0 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 3.8 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 4.2 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
Scholar 4.7 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 4.9 years ago, voted at least 25 times.
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 4.9 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
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?

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