User: James Ashmore

gravatar for James Ashmore
James Ashmore2.5k
Reputation:
2,460
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
2 hours ago
Joined:
3 years, 10 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 • 286 results • page 1 of 29 • next >
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Comment: C: Analysis of gene expression data
... If you have count data, try following one of the RNA-seq expression tutorials online. Here's a good one to start with: https://f1000research.com/articles/4-1070/v1 ...
written 28 days ago by James Ashmore2.5k
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Answer: A: Processing ATAC-seq data after peak calling
... You could look for differentially accessible regions between your treatment and control groups. The [DiffBind][1] or [csaw][2] packages can help you with this analysis. Once you have the differentially accessible regions you can start looking at genes they are close to or overlap. The [GenomicFeatur ...
written 28 days ago by James Ashmore2.5k
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Comment: C: A question about Homer ChIP-seq analysis
... Bedtools expects both files to be sorted in the same order. Sort both files by chromosome and start position: sort -k1,1 -k2,2n coverage.bedgraph > coverage_sorted.bedgraph sort -k1,1 -k2,2n peaks.bed > peaks_sorted.bed ...
written 5 weeks ago by James Ashmore2.5k
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Comment: C: A question about Homer ChIP-seq analysis
... Are you asking how to count the number of reads aligned within peak regions? If so, you can do this with Bedtools: bedtools map -a peaks.bed -b coverage.bedgraph -c 4 -o mean ...
written 5 weeks ago by James Ashmore2.5k
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Comment: C: Annotating/Finding "NNNNNN" scaffold gaps in genome assembly
... The script was written for Python 3. Either install Python 3 or try changing line 17 to : print record.id, match.start(), match.end() ...
written 5 weeks ago by James Ashmore2.5k
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Comment: C: ATAC-seq DE analysis
... Bedtools can count alignments from multiple BAM files (see http://bedtools.readthedocs.io/en/latest/content/tools/multicov.html) ...
written 5 weeks ago by James Ashmore2.5k
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Comment: C: Creating pseudo-replicates from a paired-end BAM file
... Glad to heard it still works! The script only extracts properly paired reads. Have a look how many reads are classed as properly paired in your original BAM file, and then double check the number in each of the pseudo BAM files. ...
written 7 weeks ago by James Ashmore2.5k
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Comment: C: Creating pseudo-replicates from a paired-end BAM file
... Without looking at your BAM file I can only guess that it's because you have a different version of samtools. Since writing this script there has been a few updates and I believe the way you pass in data through standard input may have changed. You don't specify which line the script fails on, if it ...
written 7 weeks ago by James Ashmore2.5k
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Comment: C: output TMM normalized counts with edgeR
... There's no need to calculate the TMM values yourself, the cpm function should do it for you given a DGEList with the *lib.size* and *norm.factors* columns present (which you get after running calcNormFactors). ...
written 7 weeks ago by James Ashmore2.5k
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Answer: A: output TMM normalized counts with edgeR
... If you run the cpm function on a DGEList object which contains TMM normalisation factors then you will get TMM normalised counts. Here is a snippet of the source code for the cpm function: cpm.DGEList <- function(y, normalized.lib.sizes=TRUE, log=FALSE, prior.count=0.25, ...) # Counts pe ...
written 7 weeks ago by James Ashmore2.5k

Latest awards to James Ashmore

Good Question 5 days ago, asked a question that was upvoted at least 5 times. For How to handle metadata in bioinformatics pipelines?
Popular Question 22 days ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Great Question 25 days ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Scholar 6 weeks 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 7 weeks 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 3 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Popular Question 3 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Appreciated 4 months ago, created a post with more than 5 votes. For A: Run multiple fastq.gz files with FastQC and yield single report?
Great Question 6 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 6 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 7 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 8 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Good Answer 8 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 9 months ago, asked a question with at least 3 up-votes. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 9 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 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 10 months ago, created a question with more than 1,000 views. For How to handle metadata in bioinformatics pipelines?
Student 11 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Scholar 11 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
Good Answer 11 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 11 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 11 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 11 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

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