User: James Ashmore

gravatar for James Ashmore
James Ashmore2.5k
Reputation:
2,500
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
1 week, 1 day ago
Joined:
4 years 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 • 287 results • page 1 of 29 • next >
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Comment: C: using bash variable in picard MarkDuplicates command
... Can you paste the error thrown by Picard? ...
written 8 weeks 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 3 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 3 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 3 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 3 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 3 months ago by James Ashmore2.5k
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Comment: C: ATAC-seq DE analysis
... Bedtools can count alignments from multiple BAM files (see http://bedtools.readthedocs.io/en/latest/content/tools/multicov.html) ...
written 3 months ago by James Ashmore2.5k
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Comment: C: Creating pseudo-replicates from a paired-end BAM file
... Glad to heard it still works! The script only extracts properly paired reads. Have a look how many reads are classed as properly paired in your original BAM file, and then double check the number in each of the pseudo BAM files. ...
written 3 months ago by James Ashmore2.5k
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Comment: C: Creating pseudo-replicates from a paired-end BAM file
... Without looking at your BAM file I can only guess that it's because you have a different version of samtools. Since writing this script there has been a few updates and I believe the way you pass in data through standard input may have changed. You don't specify which line the script fails on, if it ...
written 3 months ago by James Ashmore2.5k
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Comment: C: output TMM normalized counts with edgeR
... There's no need to calculate the TMM values yourself, the cpm function should do it for you given a DGEList with the *lib.size* and *norm.factors* columns present (which you get after running calcNormFactors). ...
written 3 months ago by James Ashmore2.5k

Latest awards to James Ashmore

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Good Question 9 weeks ago, asked a question that was upvoted at least 5 times. For How to handle metadata in bioinformatics pipelines?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Visualising the number of overlapping peaks in ChIP-seq studies
Great Question 12 weeks ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
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
Popular Question 5 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 Visualising the number of overlapping peaks in ChIP-seq studies
Appreciated 6 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 8 months ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 8 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 9 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 10 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Good Answer 10 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 11 months ago, asked a question with at least 3 up-votes. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 11 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 12 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 13 months ago, created a question with more than 1,000 views. For How to handle metadata in bioinformatics pipelines?
Student 13 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
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
Good Answer 13 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?
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
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

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