User: James Ashmore

gravatar for James Ashmore
James Ashmore2.9k
Reputation:
2,910
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
19 hours ago
Joined:
5 years, 9 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 • 296 results • page 1 of 30 • next >
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Answer: C: Batch correction in scRNA-seq data via fastMNN | pro/contra
... I would apply the mutual nearest neighbours correction for the exact reasons laid out by the developer here: https://osca.bioconductor.org/multi-sample-comparisons.html#sacrificing-differences ...
written 8 weeks ago by James Ashmore2.9k
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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 17 months ago by James Ashmore2.9k
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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 17 months ago by James Ashmore2.9k
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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 17 months ago by James Ashmore2.9k
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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 17 months ago by James Ashmore2.9k • updated 17 months ago by Pierre Lindenbaum129k
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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 21 months ago by James Ashmore2.9k
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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 21 months ago by James Ashmore2.9k
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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 21 months ago by James Ashmore2.9k
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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 21 months ago by James Ashmore2.9k • updated 20 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 23 months ago by James Ashmore2.9k

Latest awards to James Ashmore

Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: What "chrUn" stand for in UCSC genome browser web server?
Popular Question 15 days ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: What "chrUn" stand for in UCSC genome browser web server?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Using getopt module to parse and define command line arguments in python
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Scholar 8 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 11 months ago, created a question with more than 1,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Appreciated 11 months ago, created a post with more than 5 votes. For A: What "chrUn" stand for in UCSC genome browser web server?
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
Popular Question 11 months ago, created a question with more than 1,000 views. For Filtering paired and single end reads from a BAM file
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
Popular Question 11 months ago, created a question with more than 1,000 views. For Download genome annotations from UCSC's MySQL database
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Popular Question 12 months ago, created a question with more than 1,000 views. For Quick way to Identify batch effect from covariates?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Python syntax help (metaseq)
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Popular Question 16 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
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
Popular Question 18 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 19 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 19 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question 20 months ago, created a question with more than 1,000 views. For Difficulty replicating likelihood ratio test from RNA-seq paper
Appreciated 21 months ago, created a post with more than 5 votes. For A: What "chrUn" stand for in UCSC genome browser web server?

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