User: Malcolm.Cook

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Malcolm.Cook800
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kansas, usa
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Posts by Malcolm.Cook

<prev • 106 results • page 1 of 11 • next >
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Comment: C: How to design qPCR primers to validate RNA-seq experiment?
... What aspect of the mRNA-seq results are you seeking to validate? If you are trying to design primers to recapitulate the results of an *analysis* of the mRNA-seq, you should describe the analysis (and the experiment/samples/sequencing). That said, primer3 has lots of design options when you get ...
written 4 days ago by Malcolm.Cook800
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Comment: C: Normal to have high variability in Broad Institute's GSEA Output?
... that is startling - are you sure you did not reset some other parameter to the analysis? What software are you using? MIT/Broad's Java application? ...
written 4 days ago by Malcolm.Cook800
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Answer: A: meme-chip command line usage error
... I don't think the message about Log4perl is the real issue. I would expect some form of disaster passing a period in `-oc .` to meme-chip as you do. Pass in string to name the directory you want created to place the results ...
written 9 months ago by Malcolm.Cook800
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Answer: A: How to overlap the coverage profiles of read-mapping in IGV or other mapping res
... [wiggletools][1] allows to compute ratios or differences between bigwig tracks. You may wish to be working with normalized bigwigs,such as can optionally be produced by the STAR aligner, or a variety of other approaches. [1]: https://github.com/Ensembl/WiggleTools ...
written 9 months ago by Malcolm.Cook800
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Comment: C: Question about mapping motif binding sites to genome location
... That output is similar to FIMO output format as document [here][1]. But not identical. How exactly did you produce it. Did you use [retrieve-seq][2] to get your upstream sequences? What did the first line in that file look like? [1]: http://meme-suite.org/doc/fimo.html [2]: http://floresta. ...
written 9 months ago by Malcolm.Cook800
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Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
... If I had the cred to promote this comment to an "answer", I would, and up-vote it. Also see: - vcf-consensus (part of VCFtools)- "Apply VCF variants to a fasta file to create consensus sequence." - https://github.com/vcflib/vcflib ...
written 9 months ago by Malcolm.Cook800
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Answer: A: how to parse raw reads to unique reads with count for fast alignment
... see [FASTQ/A Collapser][1] Collapsing identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts) [1]: http://hannonlab.cshl.edu/fastx_toolkit/ ...
written 9 months ago by Malcolm.Cook800
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Answer: A: visualization of identified SSRs
... Assuming the output format is as presented [here][1], it looks like the output is in GFF format. The next question is, what do you mean by "visualize"? If you want to see where all these SSRs fall on the genome with respect to other annotations (genes, repeative regions, etc), you will want to loa ...
written 9 months ago by Malcolm.Cook800
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Answer: A: looking for alignment in IGV
... Is sounds like you require IGV to visually indicate which RNASeq reads in a bam file are compatible with which transcript models that they overlap, and to what extent. This is not a fully specified requirement, as it does not define "compatible" or "extent", and does not address issues such as: - ...
written 9 months ago by Malcolm.Cook800
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Comment: C: Intron size from gtf/gff file ?
... Do you possibly mean per transcript? When a "gene" has multiple isoforms/transcripts, it is not clear what is meant by the intron sequence of the gene, since the same underlying sequence can be intronic in one transcript and coding or in another. Some people intend to mean sequence which is intron ...
written 9 months ago by Malcolm.Cook800

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Centurion 9 months ago, created 100 posts.
Teacher 10 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 21 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 2.6 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 3.8 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 4.3 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
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Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 4.4 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 4.4 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
Teacher 4.4 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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