User: James Ashmore

gravatar for James Ashmore
James Ashmore2.3k
Reputation:
2,300
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Trusted
Location:
UK/Edinburgh/MRC Centre for Regenerative Medicine
Twitter:
jma1991
Last seen:
an hour ago
Joined:
3 years, 5 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 • 271 results • page 1 of 28 • next >
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Answer: A: Error in BioMartVersion
... A slightly easier and faster method would be to use the annotation packages Bioconductor provides: library("org.Hs.eg.db") entrez <- c("100422954", "100422957", "100422959", "100422962") symbol <- mapIds(org.Hs.eg.db, keys = entrez, keytype = "ENTREZID", column = "SYMBOL") ...
written 23 days ago by James Ashmore2.3k
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Comment: C: Utility of Kallisto bootstraps when not using sleuth downstream
... Bootstrapping provides a measure of the accuracy of the estimated abundances. The abundance values are consistent regardless of the number of bootstraps. See the answers [here][1]. Conventional packages such as DESeq2 or edgeR do not readily accommodate this extra information so you may as well run ...
written 26 days ago by James Ashmore2.3k
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Comment: C: Please share a link of an article on Transcriptomic analysis
... https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8 Happy reading ...
written 28 days ago by James Ashmore2.3k
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Comment: C: converting paired end reads to single end, is this a good idea?
... A single-end read comes from sequencing one end of a fragment. A paired-end reads comes from sequencing the same fragment twice (each end of the fragment is sequenced). With single-end data, a single read represents a single fragment, but with paired-end data two reads (each pair) represents a singl ...
written 28 days ago by James Ashmore2.3k
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Comment: C: converting paired end reads to single end, is this a good idea?
... As long as you remember to assign fragments to genes (with your paired-end data) rather than reads (default for single-end data) you should be okay to compare the two data sets. ...
written 28 days ago by James Ashmore2.3k
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Comment: C: Normalizing transcriptome data by tissue type
... Can you block on tissue origin? For example, the same way you might incorporate a batch effect (~ batch + group) you instead incorporate tissue origin (~ tissue + tumour) ...
written 4 weeks ago by James Ashmore2.3k
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Answer: A: Parse FASTQC data
... By default FastQC should generate a zip folder with files containing the data used for plotting. ...
written 5 weeks ago by James Ashmore2.3k
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Comment: C: Is possible to convert BSgenome object to GRange?
... A slightly quicker way: GRanges(seqinfo(BSgenome.Dmelanogaster.UCSC.dm6)) ...
written 5 weeks ago by James Ashmore2.3k
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Comment: C: Changes log2FC values of DESeq2
... Check if you need to use the lfcShrink function after calling the DESeq2 main function. In older versions DESeq2 would call lfcShrink internally, but in the latest version you have to call it yourself. ...
written 8 weeks ago by James Ashmore2.3k
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Comment: C: High Speed Downloading of SRA, SAM and Fastq Files
... You can also speed-up fastq-dump by using the parallel version: https://github.com/rvalieris/parallel-fastq-dump ...
written 8 weeks ago by James Ashmore2.3k

Latest awards to James Ashmore

Great Question 29 days ago, created a question with more than 5,000 views. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 5 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 9 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 3 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: SRA to fastq
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?
Student 4 months ago, asked a question with at least 3 up-votes. For How do I view the height / distribution of ChIP-seq peaks?
Commentator 4 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 5 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 How to handle metadata in bioinformatics pipelines?
Student 6 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Good Answer 6 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?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 6 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 6 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 6 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 6 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 7 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Scholar 7 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 7 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
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
Scholar 10 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 11 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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