User: Chris Cole

gravatar for Chris Cole
Chris Cole680
Reputation:
680
Status:
Trusted
Location:
Scotland
Twitter:
drchriscole
Last seen:
1 year, 4 months ago
Joined:
5 years, 8 months ago
Email:
c*****@dundee.ac.uk

about me

Posts by Chris Cole

<prev • 99 results • page 1 of 10 • next >
1
vote
0
answers
987
views
0
answers
Comment: C: How to map by bwa with 50 mismatches?
... Yet in that paper they don't use BWA either. Why not use their methodology and indeed their available [software][1] rather than re-invent the wheel? [1]: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer ...
written 2.1 years ago by Chris Cole680
0
votes
3
answers
2.2k
views
3
answers
Comment: C: BUSCO genome mode giving poor results
... So one problem was that Augustus was crashing consistently for some genes, but BUSCO pipes all errors to /dev/null so it was never report until I removed the /dev/null redirect. Managed to fix some of the (local) causes of failure, but am still getting core dumps for a small number genes. I am cir ...
written 2.1 years ago by Chris Cole680
1
vote
3
answers
2.2k
views
3
answers
Answer: A: BUSCO genome mode giving poor results
... I have given up on BUSCO v1.22 as it appears the Augustus step is not running correctly on our set-up for some reason. Reverting to v1.1b1 gives more sensible results (70-80% complete) in genome mode, but the results in transcriptome mode are now different when compared to v1.22. Nothing in [change ...
written 2.1 years ago by Chris Cole680
1
vote
1
answer
936
views
1
answers
Answer: A: predict deleteriousness of nonsense variants
... Have you tried VEP? It can provide a translation (and length delta) of the nonsense variant, which could help you in terms deleteriousness. http://www.ensembl.org/Homo_sapiens/Tools/VEP?db=core ...
written 2.1 years ago by Chris Cole680
0
votes
1
answer
715
views
1
answers
Comment: C: Differetial analysis after HTSEq count
... edgeR/DESeq/DESeq2/etc don't take raw reads. They take gene read counts from tools like HTseq-count or featureCounts. ...
written 2.1 years ago by Chris Cole680
1
vote
2
answers
1.5k
views
2
answers
Comment: C: error after DESeq function nbinomTest with only one replicate
... Sorry, but there's no such thing as robust unreplicated RNA-seq analysis. It's simply a qualitative assessment of a system, very little can be drawn from such an experiment. I'd argue it's a waste of money. Also in [our hands][1] NOISeq is not as good as other methods as it doesn't control FPR very ...
written 2.2 years ago by Chris Cole680
0
votes
2
answers
1.5k
views
2
answers
Answer: A: error after DESeq function nbinomTest with only one replicate
... Your problem is where you define your conditions. newCountDataset() expects a factor with your conditions, but you give it a data.frame with rownames and entries. Your cds summary has the sample names as "BC_SN PA_SN", but when you run nbinomTest(cds,"treated","untreated") you're giving it names t ...
written 2.2 years ago by Chris Cole680
0
votes
3
answers
2.2k
views
3
answers
Comment: C: BUSCO genome mode giving poor results
... I'm wanting to do both and compare the results. I've already done this with CEGMA and the results are similar. A reviewer recommended we use BUSCO instead, but now am getting these very different results. Am tempted to ditch BUSCO and just stick with CEGMA. ...
written 2.2 years ago by Chris Cole680
0
votes
3
answers
2.2k
views
3
answers
Comment: C: BUSCO genome mode giving poor results
... Hi Colin, Do have an example species that works for you and I could use as a test, please? Preferably a relatively small one for speed reasons. Thanks. ...
written 2.2 years ago by Chris Cole680
0
votes
3
answers
2.2k
views
3
answers
Comment: C: BUSCO genome mode giving poor results
... Yeah, could well be. I'm not convinced that BUSCO is doing the right thing here either, but working through the code is like walking through treacle... ...
written 2.2 years ago by Chris Cole680

Latest awards to Chris Cole

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Where are the different RAM versions of IGB in v8.3.0
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Dowloading All Protein Sequences
Scholar 2.2 years ago, created an answer that has been accepted. For A: Problems merging TopHat mapped and unmapped BAMs for submission to ENA
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Which Type Of Database Systems Are More Appropriate For Storing Information Extr
Popular Question 2.6 years ago, created a question with more than 1,000 views. For When Is A Heterozygous Call Not Heterozygous?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Which Type Of Database Systems Are More Appropriate For Storing Information Extr
Supporter 3.2 years ago, voted at least 25 times.
Scholar 3.2 years ago, created an answer that has been accepted. For A: Problems merging TopHat mapped and unmapped BAMs for submission to ENA
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Paired-End Bam Files
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: How Much Coverage Do We Need For An Rna-Seq Experiment?
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Dowloading All Protein Sequences
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: How Much Coverage Do We Need For An Rna-Seq Experiment?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Tool Recommendations For Human Genome Assembly
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: How Much Coverage Do We Need For An Rna-Seq Experiment?
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Dowloading All Protein Sequences

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 800 users visited in the last hour