User: James Ashmore

gravatar for James Ashmore
James Ashmore1.4k
Reputation:
1,350
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Location:
UK, Edinburgh
Twitter:
jma1991
Last seen:
4 hours ago
Joined:
2 years, 6 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 • 156 results • page 1 of 16 • next >
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Comment: C: Fast and reproducible method to downsample a count matrix to different sequencin
... Edit: Sorry yes that's what I mean, so setting the seed should solve that issue. No I mean if I downsample the matrix to say 1M reads per sample (column), and then I do it again, the downsampling will be slightly different across genes (rows) ...
written 1 day ago by James Ashmore1.4k
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Fast and reproducible method to downsample a count matrix to different sequencing depths?
... Maybe slightly off-topic, moderators please delete if inappropriate. Could someone recommend a package or function to downsample a count matrix? I'd like to downsample the matrix multiple times so I can test various metrics at different sequencing depths. I'm currently using a downsampling function ...
R written 1 day ago by James Ashmore1.4k
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Comment: C: Existing software to calculate RNASeq read distribution by "gene_type" (Gencode)
... Not sure about existing software, but couldn't you just transform your GTF file into a BED file and use that with RSeQC? ...
written 1 day ago by James Ashmore1.4k
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Answer: A: PC3 & PC2 using plotPCA function in R
... From what I can tell there is no way to return PC2/PC3 from the plotPCA function. Instead what you could do is just use the code from within the plotPCA function to return the full results of the principal component analysis: # calculate the variance for each gene rv <- rowVars(assay ...
written 1 day ago by James Ashmore1.4k
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Answer: A: Binning the genomic regions and counting reads
... You should be able to do all of this using bedtools. Here's an example for you to follow: bedtools slop -i regions.bed -g chrom.sizes -b 2000 > regions_2kb.bed bedtools makewindows -b regions_2kb.bed -w 500 > windows_500bp.bed bedtools coverage -counts -a windows_500bp.bed -b alig ...
written 1 day ago by James Ashmore1.4k
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Comment: C: Quantile normalization and variability questions
... I think this is incorrect. Quantile normalisation creates a reference distribution from all your samples which you use to normalise each of them separately. This is appropriate when there is small variability across groups. When there are large differences in the distributions between your groups (i ...
written 2 days ago by James Ashmore1.4k
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Comment: C: Quantile normalization and variability questions
... This paper will really help your understanding of when to use quantile normalisation: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0679-0 ...
written 2 days ago by James Ashmore1.4k
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Comment: C: fastQC - case of the anomalous last base
... That profile looks typical of data which has been trimmed for adapter sequences. Did you use cutadapt or trim_galore for the adapter trimming? Normally when I use trim_galore, the amount of overlap used to detect adapter contamination is a single base pair. This causes the last base of the reads to ...
written 5 days ago by James Ashmore1.4k
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Comment: C: mitochondrial blacklists ATAC-Seq
... I don't think the user has confused anything. The authors of ATAC-seq created a mitochondrial blacklist which represents high signal regions on the nuclear genome caused by read sequence homology with the mitochondrial genome. The [blacklist files have now been uploaded by the authors][1], so you ca ...
written 22 days ago by James Ashmore1.4k
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Comment: C: Trimmomatic - unknown trimmer?
... Perhaps remove the space between "ILLUMINACLIP:" and "TruSeq3-PE.fa". Also try manually specifying the input and output fastq files, rather than relying on the basename matching feature. ...
written 24 days ago by James Ashmore1.4k

Latest awards to James Ashmore

Popular Question 11 days ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 18 days ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 25 days 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 weeks ago, created a question with more than 1,000 views. For Trimmomatic not removing all Nextera adapters or N base calls
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How can I programmatically download the GEO DataSets of a given accession?
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
Student 9 months ago, asked a question with at least 3 up-votes. For How to handle metadata in bioinformatics pipelines?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Student 9 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 9 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Good Answer 9 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 9 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Teacher 11 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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Student 12 months ago, asked a question with at least 3 up-votes. For Resources to understand regression models for count data
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
Centurion 12 months ago, created 100 posts.
Good Answer 13 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 13 months ago, created an answer with at least 3 up-votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Appreciated 14 months ago, created a post with more than 5 votes. For A: Fix SAM flags on quality filtered paired-end BAM file
Popular Question 15 months ago, created a question with more than 1,000 views. For How can I programmatically download the GEO DataSets of a given accession?
Popular Question 15 months ago, created a question with more than 1,000 views. For How can I programmatically download the GEO DataSets of a given accession?
Popular Question 16 months ago, created a question with more than 1,000 views. For How do I view the height / distribution of ChIP-seq peaks?

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