Moderator: andrew.j.skelton73

Reputation:
5,970
Status:
Trusted
Location:
London
Twitter:
ajskelton73
Last seen:
11 hours ago
Joined:
6 years, 5 months ago
Email:
a*****************@gmail.com

about me

Posts by andrew.j.skelton73

<prev • 711 results • page 1 of 72 • next >
0
votes
0
answers
179
views
0
answers
Comment: C: Keep the paired reads whose length less than 400,000 bp
... Ah, I think you're referring to the insert size. Check out [this][1] post on filtering a bam file on insert size. Also you can use the [bbmap][2] tools to look at a histogram of your insert size for some diagnostics [1]: https://www.biostars.org/p/95822/ [2]: https://jgi.doe.gov/data-and-tools ...
written 12 weeks ago by andrew.j.skelton736.0k
1
vote
1
answer
258
views
1
answers
Answer: A: How to interpret a Stringdb interaction network of a mouse-proteomics dataset wh
... Your protein identifiers are human. Take P10809 as an example - [Uniprot Entry][1] - P10809 (CH60_HUMAN), 60 kDa heat shock protein, mitochondrial, HSPD1, Homo sapiens (Human) - [Mouse Uniprot Entry][2] - P63038 (CH60_MOUSE), 60 kDa heat shock protein, mitochondrial, Hspd1, Mus musculus (Mouse) ...
written 7 months ago by andrew.j.skelton736.0k
1
vote
2
answers
228
views
2
answers
Answer: A: Visualising individual humans in RNA-seq
... This is certainly a tricky problem. My favourite method for exploring what's happening with individual samples is [GSVA][1]. GSVA takes your expression matrix (genes x samples) and a set of gene sets (pathways, functions, whatever you like), and calculates a score that summarises the geneset for a g ...
written 7 months ago by andrew.j.skelton736.0k
0
votes
1
answer
2.1k
views
1
answers
Comment: C: cross platform microarray normalization
... Hi, @ghataksoumyakanti - This thread is nearly 4 years old. Please open a new question with lots of detail to ensure that users can help you out! - [See here for how to ask a good question][1] [1]: https://www.biostars.org/p/75548/ ...
written 8 months ago by andrew.j.skelton736.0k
0
votes
1
answer
411
views
1
answers
Comment: C: Vcf produced after ApplyVSQR step
... Can you clarify if this is WES / WGS / Targeted sequencing? ...
written 11 months ago by andrew.j.skelton736.0k
1
vote
1
answer
411
views
1
answers
Answer: A: Vcf produced after ApplyVSQR step
... I'd check out [this post][1] which tries to explain VQSR all in one. Particularly look at the *How ApplyRecalibration works in a nutshell* section: > During the first part of the recalibration process, variants in your > callset were given a score called VQSLOD. At the same time, variants &g ...
written 11 months ago by andrew.j.skelton736.0k
0
votes
1
answer
411
views
1
answers
Comment: C: Vcf produced after ApplyVSQR step
... I've formatted your post so that your code blocks are more readable ...
written 11 months ago by andrew.j.skelton736.0k
0
votes
1
answer
341
views
1
answers
Comment: C: Investigating differentially expressed genes
... Do you have the loci of each SNP in a file? Also reference genome builds may play a role here - are they different between the RNAseq and GWAS platform? ...
written 11 months ago by andrew.j.skelton736.0k
3
votes
1
answer
333
views
1
answers
Answer: A: Kolmogorov-Smirnov Test and Shapiro-Wilk Test statistics in Proteomics
... This seems like you want to understand why these "geeky" mathematical principles are relevant to statistical modelling of biological data. This is beyond proteomics, but more orientated to fundamental assumptions of modelling. I'd recommend reading Wolfgang Huber & Susan Holmes' book, Modern Sta ...
written 11 months ago by andrew.j.skelton736.0k
0
votes
1
answer
364
views
1
answers
Answer: A: How to obtain multiple sequence alignments of genomes of selected vertebrate spe
... Have you considered trying out Ensembl for this problem? Buffalo (or Bison), are available in the [MSA functionalities in Ensembl][1]. Here's a [video][2] on how to perform MSA of specific species using Ensembl tools. [1]: https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.ht ...
written 11 months ago by andrew.j.skelton736.0k

Latest awards to andrew.j.skelton73

Scholar 13 days ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Appreciated 13 days ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Scholar 21 days ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Find SNPs in the exome from WGS data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Epic Question 4 months ago, created a question with more than 10,000 views. For Illumina Instrument Type from fastq?
Great Question 4 months ago, created a question with more than 5,000 views. For Illumina Instrument Type from fastq?
Student 4 months ago, asked a question with at least 3 up-votes. For 450K - "Best" Normalisation Method?
Scholar 6 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Popular Question 9 months ago, created a question with more than 1,000 views. For Gemini Installation pybedtools version error
Scholar 10 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 11 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Appreciated 11 months ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 12 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Illumina Instrument Type from fastq?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Machine learning based classification techniques
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Machine learning based classification techniques
Appreciated 16 months ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Appreciated 17 months ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 18 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Scholar 20 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1786 users visited in the last hour