User: James Ashmore

gravatar for James Ashmore
James Ashmore2.3k
Reputation:
2,340
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Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
15 hours ago
Joined:
3 years, 8 months ago
Email:
j******@icloud.com

I am a PhD student in Simon Tomlinson's research group at the MRC Centre for Regenerative Medicine. My interests lie in the biology of reprogramming, and developing methods to analyse the reprogramming process.

Posts by James Ashmore

<prev • 276 results • page 1 of 28 • next >
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Answer: A: ATAC-seq : strategies to have the list of the expressed genes
... If you have R and Bioconductor installed, you can try the following steps: # Load required packages pkgNames <- c("rtracklayer", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene") libSetup <- lapply(pkgNames, library, character.only = TRUE) # Import narrowPeak file ...
written 13 days ago by James Ashmore2.3k
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Comment: C: ATAC-seq : strategies to have the list of the expressed genes
... Can you tell us which genome assembly you aligned your NGS data to? ...
written 13 days ago by James Ashmore2.3k
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Comment: C: Problem with getGEO
... I was able to download the file: > getGEO("GSE75970") Found 1 file(s) GSE75970_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75970/matrix/GSE75970_series_matrix.txt.gz' Content type 'application/x-gzip' length 1661409 bytes (1.6 MB) ...
written 14 days ago by James Ashmore2.3k
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Measuring insertion/deletion frequency of a small sequence motif
... I want to check how often the sequence TGAT is inserted or deleted in different strains of mouse. I downloaded VCF files containing SNPs and Indels for each strain from the Mouse Genomes Project. I can grep the indels file for my sequence and count how many times it appears in the REF/ALT columns. H ...
snp mnp written 5 weeks ago by James Ashmore2.3k
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Comment: C: Diffbind - Very high proportion of significant peaks
... If your aim is to call different open regions I'd first be concerned about using BAMPE when you call peaks. When you use BAMPE, MACS2 will create a coverage vector from the fragment (created by filling in the space between the two mapped ends). However, pairs can be mapped either side of a nucleosom ...
written 5 weeks ago by James Ashmore2.3k
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Answer: A: Error in BioMartVersion
... A slightly easier and faster method would be to use the annotation packages Bioconductor provides: library("org.Hs.eg.db") entrez <- c("100422954", "100422957", "100422959", "100422962") symbol <- mapIds(org.Hs.eg.db, keys = entrez, keytype = "ENTREZID", column = "SYMBOL") ...
written 3 months ago by James Ashmore2.3k
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Comment: C: Utility of Kallisto bootstraps when not using sleuth downstream
... Bootstrapping provides a measure of the accuracy of the estimated abundances. The abundance values are consistent regardless of the number of bootstraps. See the answers [here][1]. Conventional packages such as DESeq2 or edgeR do not readily accommodate this extra information so you may as well run ...
written 3 months ago by James Ashmore2.3k
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Comment: C: Please share a link of an article on Transcriptomic analysis
... https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8 Happy reading ...
written 3 months ago by James Ashmore2.3k
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Comment: C: converting paired end reads to single end, is this a good idea?
... A single-end read comes from sequencing one end of a fragment. A paired-end reads comes from sequencing the same fragment twice (each end of the fragment is sequenced). With single-end data, a single read represents a single fragment, but with paired-end data two reads (each pair) represents a singl ...
written 3 months ago by James Ashmore2.3k
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Comment: C: converting paired end reads to single end, is this a good idea?
... As long as you remember to assign fragments to genes (with your paired-end data) rather than reads (default for single-end data) you should be okay to compare the two data sets. ...
written 3 months ago by James Ashmore2.3k

Latest awards to James Ashmore

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Run multiple fastq.gz files with FastQC and yield single report?
Great Question 3 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Using getopt module to parse and define command line arguments in python
Scholar 5 months ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Do I have to check every fastqc to make good quality?
Student 7 months ago, asked a question with at least 3 up-votes. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Using getopt module to parse and define command line arguments in python
Popular Question 8 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 8 months ago, created a question with more than 1,000 views. For How to handle metadata in bioinformatics pipelines?
Student 9 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Do I have to check every fastqc to make good quality?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 9 months ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 9 months ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Scholar 9 months ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 10 months ago, created an answer that has been accepted. For A: Calculate the number of paired-end reads their middle size is greater than # KB
Popular Question 10 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 11 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file

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