User: Nick Crawford

gravatar for Nick Crawford
Nick Crawford200
Reputation:
200
Status:
Trusted
Location:
Philadelphia PA
Website:
http://ngcrawford.com/
Twitter:
ngcrawford
Scholar ID:
Google Scholar Page
Last seen:
3 years, 4 months ago
Joined:
8 years, 9 months ago
Email:
n*********@gmail.com

Posts by Nick Crawford

<prev • 16 results • page 1 of 2 • next >
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Comment: C: 1000 Genomes Snps' Ancestral Allele
... There are more detailed instructions about obtaining the dbSNP ancestral alleles here: http://www.ncbi.nlm.nih.gov/sites/books/NBK44409/#Build.how_do_i_download_a_flat_file_that ...
written 4.7 years ago by Nick Crawford200
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Answer: A: Ihs Score Calculation
... There's a new (2014) implementation of most of the 'EHH' algorithms that looks promising. The main caveat being that I haven't actually used it yet. "Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated ...
written 4.7 years ago by Nick Crawford200
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Comment: C: List Of Snps On Illumina Omni 5M Genotyping Array
... The linked file has only 1.13 million SNPs... ...
written 4.8 years ago by Nick Crawford200
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Answer: A: Access Hash With 250M Entries
... "Sorry for the delay but I am trying to basically remove some genes and x cM regions around the genes. I have the physical positions of the start and end of the genes and based on the genetic position, I want to remove the gene + flanking region. I agree, I can upload the sites as an array but that ...
written 5.2 years ago by Nick Crawford200
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Comment: C: Vcf Files From 1000 Genomes For Pypgen
... Pypgen author here. Sorry for the delay getting to this, but I defended my dissertation earlier this month and have been underwater. Anyway, pypgen is currently hard coded to expect a GQ field. I'll fix that in a future release. ...
written 5.8 years ago by Nick Crawford200
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Comment: C: How To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions
... I don't think that quite works. I'd like to count the number of unique gene_ids that fall with each region. I'll update my question to better explain that. ...
written 6.1 years ago by Nick Crawford200
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How To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions
... I'd like to count the number of unique genes in a gff file falling within a list of genomic regions. With bedtools I can count the number of regions within the gff which is almost what I want, but not quite. bedtools intersect -a regions.bed -b my.gff -c UPDATE: I should have made my question a ...
bedtools gtf gff written 6.1 years ago by Nick Crawford200
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Comment: C: Trying To Calculate Percent Of Mapped And Unmapped Vs.Total Reads
... I think erichpeterson is using reads mapped with bowtie2/tophat. Tophat splits the mapped and unmapped reads into separate files. The flagstat output would be super helpful, however. ...
written 6.4 years ago by Nick Crawford200
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Comment: C: Trying To Calculate Percent Of Mapped And Unmapped Vs.Total Reads
... Can you provide the numbers you get for FORWARD, REVERSE, TOT_READS, ACCEPTED, and UNMAPPED? If you're off by twofold it could be because the mapped reads are counted as pairs (bam) while you've counted each read in each pair individually (fasta). ...
written 6.4 years ago by Nick Crawford200
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Answer: A: Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
... It doesn't appear that you're setting either the -G/--GTF or the -g/--GTF-guide flags when you run cufflinks. See comments above as well. ...
written 6.4 years ago by Nick Crawford200

Latest awards to Nick Crawford

Scholar 3.6 years ago, created an answer that has been accepted. For A: Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Ensembl Gtf/Gff File Misses Obvious Rrnas
Student 4.7 years ago, asked a question with at least 3 up-votes. For How To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions
Popular Question 4.9 years ago, created a question with more than 1,000 views. For How To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions

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