User: Thomas Bradley

Reputation:
90
Status:
Trusted
Location:
UEA,Norwich,UK
Twitter:
TBradley27
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 6 months ago
Email:
t****************@gmail.com

PhD Student at University of East Anglia and Earlham Institute.

Interests are currently miRNA target prediction and gene regulation more broadly

Posts by Thomas Bradley

<prev • 37 results • page 1 of 4 • next >
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Salmon: Any downstream DEA tools which uses abundance estimate variation information?
... Dear Biostars community, I was just wondering if there are any differential expression analysis tools which can be used downstream of `Salmon`, which incorporates abundance estimate variation information when either the `--numBootstraps` or `--numGibbsSamples` are used when running `salmon quant`? ...
deseq2 salmon written 5 months ago by Thomas Bradley90
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Annotate pairwise alignment with query sequence quality scores
... Hello, I have a pairwise alignment of a reference sequence and a query sequence. The query sequence has been inferred from Sanger sequencing, and has a series of Phred quality scores associated with it. Once an alignment has been generated, I would like to annotate the alignment using the quality ...
quality scores alignment written 14 months ago by Thomas Bradley90
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Comment: C: kallisto: strand-specific and fragment length calculation
... Hello Sorry, I am a little confused by you saying that --rf-stranded is most likely the most appropriate option. For SE data, wouldn't you want to only process reads that align to the forward strand of the transcript? Or have I made an error here? ...
written 17 months ago by Thomas Bradley90
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Answer: A: Trouble running vcf2phyloviz.py
... OK - so I think the problem here is that vcf2phyloviz.py is expecting data from each sample for each record. I added the following workaround (at about line 75 in the script) in order to force the script to substitute the reference base for all samples lacking data (i.e. no SNP) for any given entry ...
written 20 months ago by Thomas Bradley90
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Trouble running vcf2phyloviz.py
... Dear Biostars community, My aim is to implement the following pipeline (albeit modified) in order to generate phylogenetic trees from whole-genome sequencing of multiple closely related bacterial samples: http://userweb.eng.gla.ac.uk/cosmika.goswami/snp_calling/SNPCalling.html However - I have a ...
vcf pyvcf vcf2phyloviz written 20 months ago by Thomas Bradley90
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Comment: C: Getting average fragment length for single end reads
... Hello, If I am not mistaken, these two pieces of software will give you statistics relating to reads and not fragments? Which although useful, it is not what is requested by kallisto ...
written 21 months ago by Thomas Bradley90
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freebayes VCF output (FREQ header)
... Hello, I need to use freebayes to generate a VCF file which has a particular format, namely the file should contain the following line in the header section: FORMAT= However, because freebayes contains a large number of options, I am not sure which options to specify in order to generate this par ...
vcf freebayes written 21 months ago by Thomas Bradley90
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Comment: C: Problem using MIRZA (miRNA target prediction tool)
... Come to think of it - I don't think the software has a usage statement in the documentation. So even if I knew more about the expression data that they want - I am still not sure that I would know how to run the tool ...
written 2.4 years ago by Thomas Bradley90
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Problem using MIRZA (miRNA target prediction tool)
... Hello, I am trying to use the MIRZA miRNA target prediction tool. NB: So far, I am only dealing with the basic MIRZA tool, and not any of its extensions such as MIRZA-G. The problem that I am having is that the tool asks me to provide miRNA expression data but it does not instruct me what units of ...
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Problems installing CONTRAfold
... Hello, I am attempting to install a bioinformatics tool called 'CONTRAfold' which is a dependency for another bioinformatics which I want to install called MIRZA. However, I seem to be having some problem compiling CONTRAfold - when I run make, I return the following error: In file included f ...
compiling mirza installation contrafold written 2.4 years ago by Thomas Bradley90

Latest awards to Thomas Bradley

Popular Question 11 months ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Popular Question 14 months ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Popular Question 14 months ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Scholar 20 months ago, created an answer that has been accepted. For A: Trouble running vcf2phyloviz.py
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Supporter 3.4 years ago, voted at least 25 times.
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

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