User: James Ashmore

gravatar for James Ashmore
James Ashmore2.5k
Reputation:
2,530
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
12 hours ago
Joined:
4 years, 2 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 • 291 results • page 1 of 30 • next >
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Comment: C: So frustrated compiling necessary packages in a linux system
... +1 for the bioconda suggestion. It really has made my work easier. ...
written 4 weeks ago by James Ashmore2.5k
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Answer: A: Finding differences in motif enrichment between ATAC peak samples?
... Take a look at the recently released diffTF (https://difftf.readthedocs.io/en/latest/index.html) - it will allow you to infer differential transcription factor binding and motif enrichment. ...
written 5 weeks ago by James Ashmore2.5k
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Comment: C: Experimental design for RNA-seq time-course with the same start and end points b
... It’s a bit of a specific example but the time-course is for iPS reprogramming - the treatment gets to the end-point faster than the control. The end-point is around 15 days from the beginning. ...
written 7 weeks ago by James Ashmore2.5k
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Experimental design for RNA-seq time-course with the same start and end points but different treatments
... I have RNA-seq data for a time-course experiment which consists of the same starting and end points but two different conditions: https://postimg.cc/DW0RzJf1 I am unsure how to correctly model the data to answer the following questions: 1. Identify differential genes between each time-point withi ...
rna-seq written 7 weeks ago by James Ashmore2.5k • updated 22 days ago by Biostar ♦♦ 20
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Comment: C: using bash variable in picard MarkDuplicates command
... Can you paste the error thrown by Picard? ...
written 3 months ago by James Ashmore2.5k
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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 5 months 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 5 months 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 months 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 months 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 months ago by James Ashmore2.5k

Latest awards to James Ashmore

Popular Question 17 days ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: What "chrUn" stand for in UCSC genome browser web server?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
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
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For How to handle metadata in bioinformatics pipelines?
Popular Question 4 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Great Question 4 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
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
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
Popular Question 7 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Popular Question 7 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Appreciated 8 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 10 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 10 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 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
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Good Answer 12 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 13 months ago, asked a question with at least 3 up-votes. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 13 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 14 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 14 months ago, created a question with more than 1,000 views. For How to handle metadata in bioinformatics pipelines?
Student 15 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Good Answer 15 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 15 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file

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