User: Malcolm.Cook

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Malcolm.Cook860
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kansas, usa
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http://www.google.com/...
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Last seen:
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8 years, 7 months ago
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Posts by Malcolm.Cook

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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 2 hours ago by Malcolm.Cook860
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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 3 hours ago by Malcolm.Cook860
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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 3 hours ago by Malcolm.Cook860
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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 6 weeks ago by Malcolm.Cook860
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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 7 weeks ago by Malcolm.Cook860
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... GenomicFeatures is fully configurable as to treatment of strand. Please advise in what way it "fails". I have found otherwise. ...
written 7 weeks ago by Malcolm.Cook860
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... Well, perhaps you want to include a real example of your problematic case. In any case, why would you want to discard one of the predictions when from your two predictions of overlapping genes on opposite strands? I just first time now looked at [Mikado](https://mikado.readthedocs.io/en/latest/i ...
written 7 weeks ago by Malcolm.Cook860
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Answer: A: How can I easily remove overlapping transcripts, keeping only longest transcript
... For starters, ncRNA probably stands for non-coding RNA so you should expect zero proteins from that sample of GFF But even if there were coding... what would be your problem? Presumably you chose mikado for its predictions.... why do you want to throw any out? (FWIW: I don't know mikado other than ...
written 7 weeks ago by Malcolm.Cook860
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Answer: A: grep whole sequences containing a specific motif in a fasta file
... if you happen to have MEME-Suite installed, you also have a very nice fasta-grep which - knows about IUPAC codes - ignores newlines and treats sequence - can emit positions or matches - your pick ...
written 8 weeks ago by Malcolm.Cook860
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Answer: A: How to design qPCR primers to validate RNA-seq experiment?
... Since your analysis of RNASeq was "at the gene level" (trying to be blind to alternative splicing), you might seek for your qPCR to similarly be so. Since you enriched for mature mRNA (poly-A selection), you might design your primers to target amplifying a constitutively expressed spliced product. ...
written 8 weeks ago by Malcolm.Cook860

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Teacher 6 weeks 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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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
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Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 4.6 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 4.6 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table

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