User: James Ashmore

gravatar for James Ashmore
James Ashmore2.1k
Reputation:
2,140
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
9 hours ago
Joined:
3 years, 2 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 • 259 results • page 1 of 26 • next >
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Comment: C: edgeR Pvalue/FDR results
... Can you post a histogram of your P-values? ...
written 11 hours ago by James Ashmore2.1k
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Set maximum insert size with BWA MEM?
... When aligning ATAC-seq reads it is helpful to specify the maximum insert size. This allows the aligner to correctly mark whether the distance between mates is "proper" and in turn will set the "PROPER_PAIR" flag in the SAM file. With Bowtie2 you can specify this size with the -X flag. Is it possible ...
bowtie2 atac-seq bwa written 2 days ago by James Ashmore2.1k • updated 2 days ago by Istvan Albert ♦♦ 74k
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Comment: C: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
... Can you post an MA plot of the samples you're comparing (using both edgeR and DESeq2). By memory edgeR and DESeq2 have different normalisation strategies, and I believe one of them is better suited to data where there is a global shift in fold change towards one condition. You'll be able to see this ...
written 5 weeks ago by James Ashmore2.1k
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Comment: C: Build Bowtie2 2.3.3.1 with make on linux 64 bit
... Could I suggest just using [bioconda][1] to install bowtie2? It'll be much easier than working out what libraries are missing and installing them yourself manually. [1]: https://bioconda.github.io/ ...
written 5 weeks ago by James Ashmore2.1k
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Comment: C: Whether to use all aligned reads (QC-passed) or only properly-paired reads from
... For differential expression, there's nothing wrong with using all the reads. After all, one mate still mapped and provides information to help quantify gene expression. Paired-reads are great for inferring splicing events, but I'm not sure they help quantify expression significantly better than usin ...
written 5 weeks ago by James Ashmore2.1k
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Creating pseudo-replicates from a paired-end BAM file
... I want to create pseudo-replicates from a paired-end BAM file (Both mates from a pair should be placed in the same BAM file). I wrote the following script to achieve this, but wondered if there was software available which already provides this functionality, or avoids loading all the BAM file into ...
bam pseudo-replicates written 7 weeks ago by James Ashmore2.1k • updated 7 weeks ago by Istvan Albert ♦♦ 74k
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Comment: C: Converting raw counts or DEseq2 output to TxDb container
... For each gene in your DESeq2 output, get its corresponding Entrez ID (using the *mapIds* function). Then map this ID to the corresponding TX NAME and just filter with this list. ...
written 8 weeks ago by James Ashmore2.1k
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Comment: C: Converting raw counts or DEseq2 output to TxDb container
... No problem, glad we solved the issue! ...
written 8 weeks ago by James Ashmore2.1k
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Comment: C: RNAseq uneven PCR bias "how to take into best take into account uneven PCR bias
... The user then runs the risk of removing actual signal, If you can unequivocally see on a PCA that those two samples are very different from their respective groups, I'd maybe include it as a batch effect in the DESeq2 model ...
written 8 weeks ago by James Ashmore2.1k
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Comment: C: Converting raw counts or DEseq2 output to TxDb container
... Okay I hope I've understood correctly, try the following: 1. Get all transcripts from your TxDB object (use *transcripts* function from GenomicFeatures package) 2. Filter these transcripts for those which are expressed 3. Export this GRanges object as a GFF file (use *export.gff* function from rtra ...
written 8 weeks ago by James Ashmore2.1k

Latest awards to James Ashmore

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Good Answer 23 days 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 7 weeks ago, asked a question with at least 3 up-votes. For How do I view the height / distribution of ChIP-seq peaks?
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
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 12 weeks ago, created a question with more than 1,000 views. For How to handle metadata in bioinformatics pipelines?
Student 3 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
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
Good Answer 3 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 3 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
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 4 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 4 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 4 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 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 5 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Commentator 7 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 8 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 8 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 8 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 8 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 8 months ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls

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