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User: James Ashmore

gravatar for James Ashmore
James Ashmore • 2.6k
Reputation:
2,650
Status:
Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
14 hours ago
Joined:
4 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 • 295 results • page 1 of 30 • next >
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Comment: C: Software to extract run information from FASTQ headers?
... Thanks Pierre - should be able to convert from JSON to CSV on the fly. ...
written 5 months ago by James Ashmore • 2.6k
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Comment: C: Software to extract run information from FASTQ headers?
... In my case I want to create read group information as explained by [GATK][1] by automating the extraction of run information and creating the read groups for each run/sample. [1]: https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups ...
written 5 months ago by James Ashmore • 2.6k
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Comment: C: Software to extract run information from FASTQ headers?
... This isn't homework. There seems to be a surprising number of edge-cases depending on which version of CASAVA was used to convert from BCL to FASTQ format. ...
written 5 months ago by James Ashmore • 2.6k
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Software to extract run information from FASTQ headers?
... Given a directory containing multiple FASTQ files, I would like to retrieve the run information from each file (e.g. flowcell, lane number, index e.t.c) and export the data to a CSV file. Before I write a script to do this myself, is anyone aware of any software which does this already? ...
fastq written 5 months ago by James Ashmore • 2.6k • updated 5 months ago by Pierre Lindenbaum ♦ 121k
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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 9 months ago by James Ashmore • 2.6k
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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 9 months ago by James Ashmore • 2.6k
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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 9 months ago by James Ashmore • 2.6k
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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 9 months ago by James Ashmore • 2.6k • updated 8 months 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 12 months ago by James Ashmore • 2.6k
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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 13 months ago by James Ashmore • 2.6k

Latest awards to James Ashmore

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Quick way to Identify batch effect from covariates?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Python syntax help (metaseq)
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Popular Question 4 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
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
Popular Question 6 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 7 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 7 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 8 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Appreciated 9 months ago, created a post with more than 5 votes. For A: What "chrUn" stand for in UCSC genome browser web server?
Popular Question 10 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 11 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For How to handle metadata in bioinformatics pipelines?
Popular Question 12 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Great Question 13 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Scholar 13 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 13 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 15 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Popular Question 16 months ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Appreciated 17 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 18 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 18 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 19 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 20 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
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