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Malcolm.Cook ♦ 1.0k
Status: New
Handle: @Malcolm.Cook266
Reputation: 1040
Email: m*********@gmail.com
Joined: 13 months ago
Google Scholar: a6QLU7wAAAAJ
Last seen: 14 months ago
Location: kansas, usa

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1
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1.1k
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A: Identify reads that span intron-exon junctions in RNA-Seq
15 months ago
Malcolm.Cook ♦ 1.0k
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443
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C: 5', 3' SS and Intron retention read count using STAR out.tab
15 months ago
Malcolm.Cook ♦ 1.0k
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348
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C: How to extract filename and change text in the same file
16 months ago
Malcolm.Cook ♦ 1.0k
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348
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C: How to extract filename and change text in the same file
16 months ago
Malcolm.Cook ♦ 1.0k
3
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2
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348
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A: How to extract filename and change text in the same file
16 months ago
Malcolm.Cook ♦ 1.0k
2
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1
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367
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A: How to subset reads from fastq file to use as test file on a script
17 months ago
Malcolm.Cook ♦ 1.0k
2
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0
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279
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A: Is there a standard file format for anchored contigs?
18 months ago
Malcolm.Cook ♦ 1.0k
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432
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C: Automating to convert multiple fastq files into one fastq file
19 months ago
Malcolm.Cook ♦ 1.0k
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1
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432
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C: Automating to convert multiple fastq files into one fastq file
19 months ago
Malcolm.Cook ♦ 1.0k
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1
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432
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C: Automating to convert multiple fastq files into one fastq file
19 months ago
Malcolm.Cook ♦ 1.0k
2
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1
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432
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A: Automating to convert multiple fastq files into one fastq file
19 months ago
Malcolm.Cook ♦ 1.0k
3
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2
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383
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A: How can keep the change in my fastq file when i use grep and sed to edit it?
19 months ago
Malcolm.Cook ♦ 1.0k
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1
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383
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C: How can keep the change in my fastq file when i use grep and sed to edit it?
19 months ago
Malcolm.Cook ♦ 1.0k
0
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1
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611
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A: gene set enrichment analysis
21 months ago
Malcolm.Cook ♦ 1.0k
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2
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585
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C: How can I easily remove overlapping transcripts, keeping only longest transcript
21 months ago
Malcolm.Cook ♦ 1.0k
1
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585
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C: How can I easily remove overlapping transcripts, keeping only longest transcript
21 months ago
Malcolm.Cook ♦ 1.0k
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585
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C: How can I easily remove overlapping transcripts, keeping only longest transcript
21 months ago
Malcolm.Cook ♦ 1.0k
2
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1
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585
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A: How can I easily remove overlapping transcripts, keeping only longest transcript
21 months ago
Malcolm.Cook ♦ 1.0k
1
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504
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A: grep whole sequences containing a specific motif in a fasta file
21 months ago
Malcolm.Cook ♦ 1.0k
1
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759
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A: How to design qPCR primers to validate RNA-seq experiment?
21 months ago
Malcolm.Cook ♦ 1.0k
0
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1
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759
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C: How to design qPCR primers to validate RNA-seq experiment?
22 months ago
Malcolm.Cook ♦ 1.0k
0
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1
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565
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C: Normal to have high variability in Broad Institute's GSEA Output?
22 months ago
Malcolm.Cook ♦ 1.0k
5
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5
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3.9k
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A: Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table
10.2 years ago
Malcolm.Cook ♦ 1.0k • updated 22 months ago
RamRS 21k
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A: How To Convert Blast Results To Gff
4.6 years ago
Malcolm.Cook ♦ 1.0k • updated 22 months ago
RamRS 21k
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899
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A: meme-chip command line usage error
2.6 years ago
Malcolm.Cook ♦ 1.0k
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665
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A: How to overlap the coverage profiles of read-mapping in IGV or other mapping res
2.6 years ago
Malcolm.Cook ♦ 1.0k
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678
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C: Question about mapping motif binding sites to genome location
2.6 years ago
Malcolm.Cook ♦ 1.0k
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597
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C: Recreating a Genomic reference (.fastq) from a BCF file
2.6 years ago
Malcolm.Cook ♦ 1.0k
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550
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A: how to parse raw reads to unique reads with count for fast alignment
2.6 years ago
Malcolm.Cook ♦ 1.0k
1
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596
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A: visualization of identified SSRs
2.6 years ago
Malcolm.Cook ♦ 1.0k
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714
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A: looking for alignment in IGV
2.6 years ago
Malcolm.Cook ♦ 1.0k
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1.1k
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C: Intron size from gtf/gff file ?
2.6 years ago
Malcolm.Cook ♦ 1.0k
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1.2k
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C: Average intron length in Drosophila melagnoster
2.6 years ago
Malcolm.Cook ♦ 1.0k
1
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1.5k
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A: Tool to generate a chain file from an agp file
2.6 years ago
Malcolm.Cook ♦ 1.0k
1
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1
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1.4k
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A: Where are .motif files from homer knownResults?
2.7 years ago
Malcolm.Cook ♦ 1.0k
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1.0k
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C: Future direction of Gene Set Enrichment Analysis
2.9 years ago
Malcolm.Cook ♦ 1.0k
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567
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C: all samples in 0 cluster
2.9 years ago
Malcolm.Cook ♦ 1.0k
4
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1.2k
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A: Average intron length in Drosophila melagnoster
2.9 years ago
Malcolm.Cook ♦ 1.0k
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C: Trying to modify new Repbase .embls to work as RepeatMasker .embl
3.0 years ago
Malcolm.Cook ♦ 1.0k
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1
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1.6k
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A: Merge two bigwig(+/- strand) files from RNA-seq
3.1 years ago
Malcolm.Cook ♦ 1.0k
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C: MISO: Extraction of splicing events from user specified gene annotation (gtf or
3.1 years ago
Malcolm.Cook ♦ 1.0k
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753
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C: define alternative splice sites
3.1 years ago
Malcolm.Cook ♦ 1.0k
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753
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C: define alternative splice sites
3.1 years ago
Malcolm.Cook ♦ 1.0k
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508
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C: Trying to use the gff_to_gtf utiilty in genomeTools
3.1 years ago
Malcolm.Cook ♦ 1.0k
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1
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753
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A: define alternative splice sites
3.1 years ago
Malcolm.Cook ♦ 1.0k
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1.3k
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C: Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
3.1 years ago
Malcolm.Cook ♦ 1.0k
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1.3k
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A: Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
3.2 years ago
Malcolm.Cook ♦ 1.0k
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955
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C: Cuffdiff promoter.diff is empty
3.3 years ago
Malcolm.Cook ♦ 1.0k
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1
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2.0k
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C: cuffdiff vs cuffnorm vs cuffquant
3.3 years ago
Malcolm.Cook ♦ 1.0k
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779
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A: problem in running vcf-consensus command
3.4 years ago
Malcolm.Cook ♦ 1.0k
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2.3k
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A: Create a UCSC chain file from a VCF
3.4 years ago
Malcolm.Cook ♦ 1.0k
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2.2k
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C: The most popular Alternative to David?
3.4 years ago
Malcolm.Cook ♦ 1.0k
1
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1
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958
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A: How to sequentially replace a string with numerical value?
3.5 years ago
Malcolm.Cook ♦ 1.0k
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958
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C: How to sequentially replace a string with numerical value?
3.5 years ago
Malcolm.Cook ♦ 1.0k
0
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1
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958
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C: How to sequentially replace a string with numerical value?
3.5 years ago
Malcolm.Cook ♦ 1.0k
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958
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C: How to sequentially replace a string with numerical value?
3.5 years ago
Malcolm.Cook ♦ 1.0k
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1.2k
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C: How are tss_id gtf attributes determined? How do they relate to TSS annotations?
3.6 years ago
Malcolm.Cook ♦ 1.0k
2
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1.2k
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A: How are tss_id gtf attributes determined? How do they relate to TSS annotations?
3.6 years ago
Malcolm.Cook ♦ 1.0k
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C: fetch particular columns from csv files
3.8 years ago
Malcolm.Cook ♦ 1.0k
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878
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A: Subset multiple FASTA with a set of intervals provided in a BED/GFF file?
3.9 years ago
Malcolm.Cook ♦ 1.0k
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2.6k
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C: About GFF validation
3.9 years ago
Malcolm.Cook ♦ 1.0k
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2.1k
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A: How to verify the information stored in a GFF file
3.9 years ago
Malcolm.Cook ♦ 1.0k
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2.8k
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C: Mapping refseq transcripts to encoded proteins (NM_ to NP_)
4.0 years ago
Malcolm.Cook ♦ 1.0k
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1.9k
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C: biomartian enables querying BioMart from the command line - now all Python!
4.0 years ago
Malcolm.Cook ♦ 1.0k
2
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833
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A: Suggest software for flow cytometry data analysis
4.0 years ago
Malcolm.Cook ♦ 1.0k
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762
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A: A complex situation to retreive subset of sequence data
4.1 years ago
Malcolm.Cook ♦ 1.0k
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878
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A: Expression levels in IGV
4.1 years ago
Malcolm.Cook ♦ 1.0k
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C: Convert GenBank Nocleotide Accession to Gene Symbols
4.5 years ago
Malcolm.Cook ♦ 1.0k
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A: How to convert .gb to fasta (.fa, .fasta format) and is it correct?
4.6 years ago
Malcolm.Cook ♦ 1.0k
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36k
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C: Sequence Length Distribution From A Fastq File
4.6 years ago
Malcolm.Cook ♦ 1.0k
2
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1
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6.1k
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A: How to add tss_id and p_id in an Ensembl GTF (or any GTF other than that generat
4.7 years ago
Malcolm.Cook ♦ 1.0k
0
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6.7k
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A: Convert multiple-sequence fasta file to single long sequence
4.9 years ago
Malcolm.Cook ♦ 1.0k
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12k
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A: Hello, How We Can Convert Human Entrez Gene Ids Into Mouse Gene Ids
5.0 years ago
Malcolm.Cook ♦ 1.0k
2
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1
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3.3k
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A: convert mouse genes to human ortholog
5.0 years ago
Malcolm.Cook ♦ 1.0k
0
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1.1k
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A: Tool to retrieve regions with reads?
5.1 years ago
Malcolm.Cook ♦ 1.0k
0
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1
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3.6k
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C: Is there a way to access the data stored in a .ab1 file ?
5.6 years ago
Malcolm.Cook ♦ 1.0k
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2
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3.6k
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C: Is there a way to access the data stored in a .ab1 file ?
5.6 years ago
Malcolm.Cook ♦ 1.0k
0
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1
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3.6k
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C: Is there a way to access the data stored in a .ab1 file ?
5.6 years ago
Malcolm.Cook ♦ 1.0k
7
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3.6k
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A: Is there a way to access the data stored in a .ab1 file ?
5.6 years ago
Malcolm.Cook ♦ 1.0k
2
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1.2k
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C: How do you organize your articles?
5.7 years ago
Malcolm.Cook ♦ 1.0k
0
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1
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8.0k
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C: how to get intronic and intergenic sequences based on gff file?
5.8 years ago
Malcolm.Cook ♦ 1.0k
4
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8.0k
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A: how to get intronic and intergenic sequences based on gff file?
5.8 years ago
Malcolm.Cook ♦ 1.0k
4
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1
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2.0k
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A: Dataset's name in BioMart for S. pombe
6.1 years ago
Malcolm.Cook ♦ 1.0k
2
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2
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5.7k
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A: Merge Files (Adding File Names To Sequence Names)
6.6 years ago
Malcolm.Cook ♦ 1.0k
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2.4k
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C: Getting Annotation Data From A Gff File
6.7 years ago
Malcolm.Cook ♦ 1.0k
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1
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2.0k
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C: Getting Rna Sequences From Gff And Fa Files
6.9 years ago
Malcolm.Cook ♦ 1.0k
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1
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2.0k
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A: Getting Rna Sequences From Gff And Fa Files
6.9 years ago
Malcolm.Cook ♦ 1.0k
0
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2.7k
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A: Software For Aligning Cdna Onto Reference Genomic Sequences To Retrieve Introns
7.0 years ago
Malcolm.Cook ♦ 1.0k
1
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1
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7.4k
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A: How To Merge Isoforms For A Gene
7.2 years ago
Malcolm.Cook ♦ 1.0k
1
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2.5k
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C: Is There A Package To Map Primer Pair On Genome In R/Bioconductor?
7.4 years ago
Malcolm.Cook ♦ 1.0k
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0
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2.6k
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A: How To Get Junctions File Using Gsnap
7.6 years ago
Malcolm.Cook ♦ 1.0k
1
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2.0k
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A: Obtaining Junctions.Bed File From Aligners Such As Gsnap
7.6 years ago
Malcolm.Cook ♦ 1.0k
1
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2.0k
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A: Retrieving Conserved Domains For Transcripts From Cdd
7.8 years ago
Malcolm.Cook ♦ 1.0k
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29k
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C: Extract Cds Fastas From A Gff Annotation + Reference Sequence
8.1 years ago
Malcolm.Cook ♦ 1.0k
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29k
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C: Extract Cds Fastas From A Gff Annotation + Reference Sequence
8.1 years ago
Malcolm.Cook ♦ 1.0k
8
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2
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29k
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A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
8.1 years ago
Malcolm.Cook ♦ 1.0k
0
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2.3k
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C: Computing Relative Coordinates Of One Bioconductor Granges Object To Another?
8.2 years ago
Malcolm.Cook ♦ 1.0k
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1
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2.3k
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C: Computing Relative Coordinates Of One Bioconductor Granges Object To Another?
8.2 years ago
Malcolm.Cook ♦ 1.0k
2
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1
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2.3k
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A: Computing Relative Coordinates Of One Bioconductor Granges Object To Another?
8.2 years ago
Malcolm.Cook ♦ 1.0k
1
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C: Can A Cds Be Also An Intron?
8.3 years ago
Malcolm.Cook ♦ 1.0k
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