User: bob-lowlow

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bob-lowlow40
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Posts by bob-lowlow

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Tophat Singletons And Problems For Converting From Bam To Fastq
... Hi all, I'm trying to get my tophat output without singletons (I'm trying to convert the output back into fastq format so everything needs a mate) but even with both the no-mixed and no-discordant options in tophat, samtools flagstat is still identifying millions of singletons, which are then esse ...
tophat bam fastq written 7.8 years ago by bob-lowlow40
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Which Database To Use For Searching Rna-Seq Reads?
... Hi All, I have some RNA-Seq reads and I was wondering which version of blast should I use to search it? e.g. is it tblastx or is there some other database or algorithm to use?? thanks ...
rna-seq written 7.8 years ago by bob-lowlow40 • updated 3.6 years ago by Biostar ♦♦ 20
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Comment: C: Converting Tophats Bam Output Back To Separate Paired End Read Fastq Files
... Thank you very much sir. ...
written 7.9 years ago by bob-lowlow40
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Converting Tophats Bam Output Back To Separate Paired End Read Fastq Files
... Hi all, I was wondering if anyone could offer me some advice on using paired end reads with Tophat, specifically with the output. I'm planning on using Tophat as part of a pipeline for processing my sequence data. The reads that map are obviously going to be easy to deal with, but the unmapped.bam ...
bioinformatics tophat bam sam rna-seq written 7.9 years ago by bob-lowlow40 • updated 7.9 years ago by Sean Davis26k
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Answer: A: How To Derive Pan Proteome
... I don't really understand what you mean? How will 784 blasts give you the pan proteome? but if you want to save on blasting stuff, assuming you have amino acid sequence information, you can use this http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi it's essentially batch blasting ...
written 7.9 years ago by bob-lowlow40
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Why Is There Lack Of Go Terms With A Prokaryotic Genome.
... Hi I'm using Blast2Go to annotate and compare the core genome and the whole genome of a species of bacteria (Pseudomonas fluorescens). For the approximately 6000 genes only about 500 of them have GO terms, and 400 of them are in the core genome (which is approx 2000 genes). I was just wondering if a ...
deleted-post written 8.2 years ago by bob-lowlow40 • updated 8.2 years ago by Istvan Albert ♦♦ 85k
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Comment: C: What Does The Score In The Orthomcl Output Represent?
... Sorry but once again I have to say that no where there does it state what the score in the output is? ...
written 8.3 years ago by bob-lowlow40
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Comment: C: What Does The Score In The Orthomcl Output Represent?
... I already checked that and it doesn't seem to say anywhere. Unless I'm missing something, in which case could you point it out? ...
written 8.3 years ago by bob-lowlow40
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What Does This Error From Cvtree Mean?
... CVTree get files' type by file(linux command), Check your file type please. Make sure your file can be recognised as 'ASCII' or 'text' by file(linux command)) I've been getting this when I upload certain files. The weird thing is I uploaded the same files several days ago and was able to make a tre ...
phylogenetics written 8.3 years ago by bob-lowlow40 • updated 8.3 years ago by Pierre Lindenbaum131k

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