User: Thomas

gravatar for Thomas
Thomas100
Reputation:
100
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Trusted
Location:
Cambridge, UK
Last seen:
1 week, 2 days ago
Joined:
4 years, 8 months ago
Email:
t****************@gmail.com

Posts by Thomas

<prev • 39 results • page 1 of 4 • next >
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Answer: A: which is better for rna-seq analysis? R or python?
... All the best packages for RNA-Seq analysis are written for R rather than python - e.g. Sleuth, DeSeq2 etc. R is primarily designed for data analysis. Python isn't. And I am of the opinion that it is always better to work with your programming language, rather than use that language for something it ...
written 3 months ago by Thomas100
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Comment: C: Problem starting and running Gmaj (MAF file viewer and manipulator)
... Hi cssuliv, I am afraid I never managed to resolve this issue. I emailed the first author of the paper but never received a reply. Best wishes, Thomas ...
written 4 months ago by Thomas100
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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 19 months ago by Thomas100 • updated 5 months ago by ATpoint38k
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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 2.4 years ago by Thomas100
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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 2.6 years ago by Thomas100
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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 2.8 years ago by Thomas100
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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 2.8 years ago by Thomas100
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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 2.9 years ago by Thomas100
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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 2.9 years ago by Thomas100
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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 3.6 years ago by Thomas100

Latest awards to Thomas

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Calculate mirSVR scores for custom sequences?
Voter 4 months ago, voted more than 100 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For Potential bug in mafsInRegion?
Popular Question 15 months ago, created a question with more than 1,000 views. For Calculate mirSVR scores for custom sequences?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Scholar 2.8 years ago, created an answer that has been accepted. For A: Trouble running vcf2phyloviz.py
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Supporter 4.6 years ago, voted at least 25 times.
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.

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