User: James Ashmore

gravatar for James Ashmore
James Ashmore1.7k
Reputation:
1,700
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
9 hours ago
Joined:
2 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 • 206 results • page 1 of 21 • next >
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Comment: C: Does read counts for ATAC-seq differential detection make sense?
... It's an interesting point, but I struggle to understand what 'background' in an ATAC-seq experiment represents. In ChIP-seq background is non-specific pull-down which generally correlates with open chromatin regions. In ATAC-seq you're specifically looking for signal in open chromatin regions. In th ...
written 19 hours ago by James Ashmore1.7k
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Comment: C: Calculate the fraction of genome that is feature X
... I've updated my answer with methods to get different features. ...
written 1 day ago by James Ashmore1.7k
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Answer: A: Calculate the fraction of genome that is feature X
... Here's an example to calculate the percentage of exonic nucleotides in the Drosophila genome. For this answer you'll need the relevant TxDb package installed: # Load relevant package library("TxDb.Dmelanogaster.UCSC.dm3.ensGene") # Create a GRanges object containing the chromosome ...
written 1 day ago by James Ashmore1.7k
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Comment: C: Best databases for Chip-Seq
... You could also try [Cistrome DB][1] [1]: http://cistrome.org/db/#/ ...
written 2 days ago by James Ashmore1.7k
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Comment: C: Bedtools intersect QTL animalgenome
... Could you post a small example of your -a and -b files please? ...
written 2 days ago by James Ashmore1.7k
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Answer: A: Add head to coverage output for many files
... You could also use the bedtools suite to create your coverage matrix with header information: Calculate read coverage across the entire genome for multiple BAM files: bedtools genomecov -bga -i sample1.bam -g genome.txt > sample1_genomecov.bedGraph bedtools genomecov -bga -i sample2.bam ...
written 2 days ago by James Ashmore1.7k
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Comment: C: Removing PCR duplicates - fastq or BAM?
... Interesting and quite surprising, I'll double-check my data ...
written 2 days ago by James Ashmore1.7k
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Comment: C: How to automatically find the right species name when there are typos, using Ent
... Not sure how to get the full list of species in NCBI, but when you manage to do that, you can use the difflib library in Python to get close matching words (credit to David Robinson): https://stackoverflow.com/questions/11563615/matching-incorrectly-spelt-words-with-correct-ones-in-python?rq=1 ...
written 2 days ago by James Ashmore1.7k
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Comment: C: Removing PCR duplicates - fastq or BAM?
... Have you got a reference for that? I've read that Picard's MarkDuplicates can handle inter-chromosomal pairs and Samtool's rmdup cannot: 1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965708/ 2. https://sourceforge.net/p/picard/wiki/Main_Page/#q-what-is-the-difference-between-markduplicates-and ...
written 2 days ago by James Ashmore1.7k
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Answer: A: Need to extract sequences from genome fasta (SeqIO object) into output file usin
... Make yourself a BED file containing the regions you want to extract and then try the [bedtools getfasta][1] command: bedtools getfasta [OPTIONS] -fi -bed [1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 3 days ago by James Ashmore1.7k

Latest awards to James Ashmore

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 22 days 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 24 days ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Commentator 3 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 3 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 3 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 3 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Popular Question 4 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 4 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Popular Question 6 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 6 months ago, created a question with more than 1,000 views. For How can I programmatically download the GEO DataSets of a given accession?
Commentator 12 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
Student 12 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Appreciated 13 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Student 13 months ago, asked a question with at least 3 up-votes. For Resources to understand regression models for count data
Guru 13 months ago, received more than 100 upvotes.
Appreciated 13 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Run multiple fastq.gz files with FastQC and yield single report?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.

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