User: James Ashmore

gravatar for James Ashmore
James Ashmore2.0k
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Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
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5 hours ago
Joined:
3 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 • 242 results • page 1 of 25 • next >
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Generate ROC curve for RNA-seq/qRT-PCR data
... I'm trying to generate a ROC curve for different RNA-seq normalisations, using qRT-PCR data for comparison. I want to define True Positives from the RNA-seq data as genes which are measured as significantly differentially expressed (FDR < 0.05) in the same direction (logFC) from the qRT-PCR data. ...
R roc rna-seq written 11 days ago by James Ashmore2.0k
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Answer: A: Extracting fasta file according to Ids
... Index your FASTA file: samtools faidx input.fasta Then get ids which start with "NM" and pipe them into samtools faidx to retrieve only those sequences: cut -f 1 input.fasta.fai | egrep "^NM" | xargs samtools faidx input.fasta > result.fasta ...
written 19 days ago by James Ashmore2.0k
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Comment: C: What does Picard tools cleansam and fixemate exactly do and what are the equival
... As far as I know the fix mate command will check that two mates of a pair are actually in the file. Sometimes prior filtering will remove one mate of a pair, but it won't update the SAM flag which says both mates are present. Fix mate will run through the file and update the flag if it can't find th ...
written 19 days ago by James Ashmore2.0k
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Answer: A: How to delete everything after a certain point in GFF3 file - PYTHON
... Lets try with an example file (using line numbers instead of actual GFF content): $ cat test.gff 1 2 3 4 5 6 7 8 9 ##FASTA 11 12 13 14 15 Find the line number which the pattern first '##FASTA' appears (for example say line 10): ...
written 19 days ago by James Ashmore2.0k
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Comment: C: Best way to compare expression values between two groups
... If you look at the "Building the results table" section of that workflow you'll see that the "results" function will give you a table of genes which are either up- or down- regulated in either group. ...
written 19 days ago by James Ashmore2.0k
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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... I can't find an explicit reference to a description argument in the ballgown constructor function so it must be an error from a function called within the ballgown constructor function. When you run R what is your working directory? The ballgown constructor function will look for data files in a sub ...
written 19 days ago by James Ashmore2.0k
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Comment: C: Best way to compare expression values between two groups
... Okay I'm slightly confused, it sounds like you want to do a differential expression analysis (an example of which you can find in the workflow I linked). Is that correct? ...
written 19 days ago by James Ashmore2.0k
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Comment: C: Best way to compare expression values between two groups
... Do you have access to the raw read counts? If so, please read https://f1000research.com/articles/4-1070/v2 ...
written 19 days ago by James Ashmore2.0k
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Comment: C: End coordinate bigger than chromosome size converting bedgraph to bigwig/ Setti
... Download the bedClip tool from the [UCSC utilities webpage][1]. Run this on your bedGraph file and it should remove those features which are running off the end of your chromosomes [1]: http://hgdownload.soe.ucsc.edu/admin/exe/ ...
written 20 days ago by James Ashmore2.0k
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Comment: C: Data retrieval from GEO
... I guess you could just use the grep command line tool to retrieve the GSE numbers: grep "Series:" ...
written 20 days ago by James Ashmore2.0k

Latest awards to James Ashmore

Popular Question 22 days ago, created a question with more than 1,000 views. For How to handle metadata in bioinformatics pipelines?
Student 4 weeks ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 5 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
Good Answer 5 weeks 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 5 weeks ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 6 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
Scholar 7 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
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 11 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 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 3 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
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
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
Teacher 5 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
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
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
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
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 How can I programmatically download the GEO DataSets of a given accession?
Commentator 14 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 14 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?

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