User: Thomas

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Thomas90
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Posts by Thomas

<prev • 36 results • page 1 of 4 • next >
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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 6 weeks ago by Thomas90
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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 4 months ago by Thomas90
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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 6 months ago by Thomas90
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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 6 months ago by Thomas90
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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 8 months ago by Thomas90
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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 8 months ago by Thomas90
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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 16 months ago by Thomas90
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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 ...
mirza mirna expression mirna target prediction written 16 months ago by Thomas90
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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 16 months ago by Thomas90
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Comment: C: Potential bug in mafsInRegion?
... Thank you Matthew - sorry, I have only just seen your message. I will look into this and get back to you. Cheers, Thomas ...
written 16 months ago by Thomas90

Latest awards to Thomas

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Scholar 6 months ago, created an answer that has been accepted. For A: Trouble running vcf2phyloviz.py
Popular Question 11 months ago, created a question with more than 1,000 views. For Cufflinks gffread utility
Supporter 2.4 years ago, voted at least 25 times.
Autobiographer 2.5 years ago, has more than 80 characters in the information field of the user's profile.

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