User: Pi

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Pi510
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510
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Last seen:
9 years ago
Joined:
9 years, 3 months ago
Email:
u1694

Into anything sports related. My proudest achievements are running 2 half marathons after a leg injury which stopped me running for 10 years. I also enjoy pottery and have more fruit bowls than any normal person should have.

Posts by Pi

<prev • 73 results • page 1 of 8 • next >
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Answer: A: Exon-Start Same As Exon-End From Ucsc Knowngene
... Could it be intron retention? ...
written 9.1 years ago by Pi510
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Gtf2.2 Validation And Conversion
... Greetings Can anyone recommend a GTF2.2 validator? There is a link to one on this page but linked page doesn't appear to be working. There is also another validator here but there isn't a readme file so I don't know if it is validating GTF2.2 or earlier version of the file format. Also on the GTF2 ...
gtf conversion written 9.1 years ago by Pi510 • updated 7.0 years ago by Biostar ♦♦ 20
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Comment: C: How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Perfor
... I know about the fondness for notebooks - especially square paper ones!! I document my work in a similar fashion to you (though I don't think I'm quite as rigorous) and have an accompanying text file explaining the process. However I can't impose conventions on other members of my team as I don't th ...
written 9.1 years ago by Pi510
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Comment: C: Help Understanding Pileup Format
... thanks again. i have read the docs for pileup but cant find any details about the default filtering you refer to? ...
written 9.1 years ago by Pi510
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Masked Or Unmasked Dna Reference For Sam2Vcf.Pl
... Hello I am converting pileup to vcf using sam2vcf. The tools says I need the reference sequence when indels are present. Whilst downloading the reference dna sequence in fasta format from ensembl the readme states the dna is available in these formats * 'dna' - unmasked genomic DNA sequences. * ...
vcf samtools pileup written 9.1 years ago by Pi510 • updated 4.8 years ago by Biostar ♦♦ 20
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Comment: C: How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Perfor
... oh that's very good then. When i did the tutorials i remember that workflows can be shared between users. It would be very good to share datasets too? That would be perfect to have workflows with named datasets showing an explicit history of how they were created. They have added a lot more to galax ...
written 9.1 years ago by Pi510
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Comment: C: How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Perfor
... i have edited the question. This does seem like a possibility.It looks like you can do things like BWA on galaxy. If galaxy doesn't have a feature you want (VCFTools, plink/seq) i guess you can add them as tools? ...
written 9.1 years ago by Pi510
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How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
... Hello Is there an online log book which can be used by a team of people analysing a data set to store details of the pipelines performed (commands, software version) on a set of data. I forever seem to be asking colleagues of how they generated the data they hand me and it seems more than prudent t ...
data galaxy written 9.1 years ago by Pi510 • updated 5.6 years ago by Biostar ♦♦ 20
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Comment: C: Non Coding, Synonymous Snp Prediction Tool ?
... Not sure i understand this comment - you can see on the screenshot (http://snpeff.sourceforge.net/) that it predicts all the consequences of a SNP that can currently be done reliably (i.e. it can say that a snp is synonymous or non synonymous but doesn't predict if the SNP is in something like an mi ...
written 9.1 years ago by Pi510
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Comment: C: Help Understanding Pileup Format
... I should point out a sam file was created with BWA. Variants were called with pileup -c option. I don't have the raw data, only the pileup ...
written 9.1 years ago by Pi510

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