User: James Ashmore
James Ashmore • 3.0k
- Reputation:
- 3,000
- Status:
- Trusted
- Location:
- UK/Edinburgh/MRC Centre for Regenerative Medicine
- Twitter:
- jma1991
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 6 years, 1 month 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
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4
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... 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 5 months ago by
James Ashmore • 3.0k
0
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1
answer
879
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1
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... Thanks Pierre - should be able to convert from JSON to CSV on the fly. ...
written 21 months ago by
James Ashmore • 3.0k
1
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1
answer
879
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1
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... 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 21 months ago by
James Ashmore • 3.0k
0
votes
1
answer
879
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1
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... 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 21 months ago by
James Ashmore • 3.0k
5
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1
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879
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7 follow
1
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... 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? ...
written 21 months ago by
James Ashmore • 3.0k
• updated
21 months ago by
Pierre Lindenbaum ♦ 131k
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4
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1.1k
views
4
answers
... +1 for the bioconda suggestion. It really has made my work easier. ...
written 2.0 years ago by
James Ashmore • 3.0k
0
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2
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1.6k
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2
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... 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 2.0 years ago by
James Ashmore • 3.0k
0
votes
0
answers
1.2k
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0
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... 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 2.1 years ago by
James Ashmore • 3.0k
1
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0
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1.2k
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0
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... 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 ...
written 2.1 years ago by
James Ashmore • 3.0k
• updated
2.0 years ago by
Biostar ♦♦ 20
2
votes
2
answers
1.3k
views
2
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... Can you paste the error thrown by Picard? ...
written 2.3 years ago by
James Ashmore • 3.0k
Latest awards to James Ashmore
Good Answer
3 months 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
4 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: What "chrUn" stand for in UCSC genome browser web server?
Commentator
5 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
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How do I view the height / distribution of ChIP-seq peaks?
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: What "chrUn" stand for in UCSC genome browser web server?
Scholar
15 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 Filtering paired and single end reads from a BAM file
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Splitting even length BED records by an even number of base-pairs produces a single base-pair window
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
15 months ago,
created a question with more than 1,000 views.
For Download genome annotations from UCSC's MySQL database
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Quick way to Identify batch effect from covariates?
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Python syntax help (metaseq)
Popular Question
20 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 Visualising the number of overlapping peaks in ChIP-seq studies
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Difficulty replicating likelihood ratio test from RNA-seq paper
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Difficulty replicating likelihood ratio test from RNA-seq paper
Appreciated
2.1 years 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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