User: James Ashmore

gravatar for James Ashmore
James Ashmore1.5k
Reputation:
1,520
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Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
2 hours ago
Joined:
2 years, 8 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 • 184 results • page 1 of 19 • next >
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Comment: C: Getting average fragment length for single end reads
... If you have single-end reads and don't have the Bioanalyzer output there is no way to calculate the actual fragment length. Instead just use a predicted value typical of most sequencing machines, say ~200bp? ...
written 6 days ago by James Ashmore1.5k
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Answer: A: SRX from SRR IDs
... With [E-utilities][1] installed you can use the following command: esearch -db sra -query SRR1294518 | esummary | xtract -pattern DocumentSummary -element Run@acc Experiment@acc [1]: https://www.ncbi.nlm.nih.gov/books/NBK25500/ ...
written 10 days ago by James Ashmore1.5k
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Comment: C: How to repeat a row for each value of its corresponding column
... Hi ak93sharma, This is more of a general programming question, rather than a bioinformatics specific question. In future questions like these should be posted to stack-overflow or similar forums. Regardless, here's a [link][1] to a quick Python script to do what you want. Have a good day. [1]: ...
written 18 days ago by James Ashmore1.5k
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Comment: C: Shifting reads for ATAC-seq alignments
... You can use bedtool's getfasta command: bedtools bamtobed -i input.bam | bedtools getfasta -fi genome.fasta -bed stdin > fragments.fasta ...
written 19 days ago by James Ashmore1.5k
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Comment: C: Appropriate statistical test for overlap analyses?
... Bedtools has three commands to test for statistical relationships (jaccard, reldist and fisher) between feature files. ...
written 26 days ago by James Ashmore1.5k
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Comment: C: Reads not assigned to features in featureCounts software
... I'm analysing sequencing data from DNA which has been digested at a specific sequence motif. The reads should all align within the windows created by this digestion. I forgot to mention I actually filtered my BAM file previously to feature counting using BEDtools. Where I removed any reads not 100% ...
written 28 days ago by James Ashmore1.5k
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Answer: A: Blacklisted regions for mm10
... Select mm10 in the drop-down box https://www.encodeproject.org/annotations/ENCSR636HFF/ ...
written 29 days ago by James Ashmore1.5k
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Reads not assigned to features in featureCounts software
... **:: I cross-posted this question on the Bioconductor support forum (after posting here) because the featureCounts website suggests that forum would be best for getting help with the featureCounts software ::** I am using featureCounts (version 1.5.2) to count the number of reads within bins along ...
featurecounts subread written 29 days ago by James Ashmore1.5k
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Answer: A: Looking for wig base coverage file for hg19
... http://www.imagenix.com/uniqueome/downloads/ ...
written 4 weeks ago by James Ashmore1.5k
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Comment: C: Speed up Picard MarkDuplicates or any better software?
... MarkDuplicates supports multiple GC threads.. -XX:ParallelGCThreads= ...
written 4 weeks ago by James Ashmore1.5k

Latest awards to James Ashmore

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Commentator 8 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
Scholar 8 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 8 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
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
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
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
Teacher 12 weeks 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 How can I programmatically download the GEO DataSets of a given accession?
Commentator 10 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 11 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Student 11 months ago, asked a question with at least 3 up-votes. For Resources to understand regression models for count data
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Appreciated 12 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Good Answer 12 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 12 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
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
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.
Student 14 months ago, asked a question with at least 3 up-votes. For Resources to understand regression models for count data
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
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Good Answer 15 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?

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