User: John David Osborne

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Posts by John David Osborne

<prev • 15 results • page 1 of 2 • next >
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Snpeff - Reports Gain Of Stop Codon As Frame_Shift In Some Cases
... Hi Pablo, Correct me if I am wrong, but I believe that SNPEff doesn't check the inserted sequence when computing the effect of an insertion? For instance an insertion of TTTA will be reported as a frameshift mutation. In the majority of cases this is fine, however if the current reading frame from ...
snp snpeff written 6.8 years ago by John David Osborne160 • updated 6.7 years ago by Jennifer Hillman Jackson25k
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Snpeff 2.0.2 Wrapper Problem / Partial Fix
... Hi Pablo, We recently installed 2.0.2 SnpEff at the UAB Galaxy instance (thanks for adding those mycoplasma genomes to SNPEff!) but we ran into some problems with the galaxy wrapper. It looks like it is for an older version of SnpEff and it chocks on the input options it is fed. I replaced the inp ...
snp snpeff written 7.0 years ago by John David Osborne160
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Comment: C: Genbank Submission - How To Generate Fasta (Not Fastq) Files
... Thanks for your reply Jen. I managed to use Pileup-to-Interval (on my new strain) and then Extract Genomic DNA but I'm not too sure what I got in terms of a FASTA file. What I am looking for is a consensus file for my sequence that can be submitted to Genbank, not a interval on a reference strain. ...
written 7.2 years ago by John David Osborne160
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Comment: C: Extract Genomic Dna Problem
... Hi Jen, Where do you get your AXT or NIB files in order to do the extract genome operation? I understand that extract genomic DNA is dependent on those files and correct paths/files in AlignSec.loc? This is for our local instance of Galaxy. -John ________________________________________ To: S ...
written 7.3 years ago by John David Osborne160
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Axt And Nib Files For Alignseq.Loc
... I was wondering how to get a hold of the axt and/or nib files required by alignseq.loc. It's not mentioned on the local NGA Galaxy setup page. I was surprised to learn that: "Fetch Sequences -> Extract Genomic DNA" requires AXT or NIB alignment files in order to extract mouse genomic DNA from B ...
galaxy written 7.3 years ago by John David Osborne160 • updated 7.2 years ago by Jennifer Hillman Jackson25k
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Genbank Submission - How To Generate Fasta (Not Fastq) Files
... I still haven't found an easy solution to this problem and I am afraid I'm going to have to write one my own - which makes little sense as I bet this has been solved thousands of times! Can anybody point me to a script/software to convert a samtools pileup file into a fasta consensus file? It would ...
bam samtools written 7.3 years ago by John David Osborne160 • updated 7.3 years ago by Jennifer Hillman Jackson25k
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Answer: A: Converting Transcriptomes To Proteomes
... Hi David, I've successfully used SNPEff (which can fit into galaxy) to make SNP effect predictions that would effect the proteome, but from genomic not transcriptomic data but I think it might still work on that... It takes in pileup/vcf format and predicts coding changes, upstream changes, splice ...
written 7.3 years ago by John David Osborne160
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Aligning Against Multiple Reference Sequences
... Are there any tools in Galaxy to align short reads against multiple reference sequences? I have a dozen microbial genomes sequenced for which there are 2 reference genomes already sequenced. We have tried aligning each of these individually against either of the reference genomes - some align bette ...
galaxy written 7.3 years ago by John David Osborne160 • updated 7.3 years ago by David Matthews630
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Comment: C: Fastq Groomer And Compute Quality Statistics
... Thanks Ross, I don't see it under my local install - are there any pre-written scripts to integrate it with a local galaxy instance? I assume you are talking about this tool here: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ -John ________________________________________ To: John David ...
written 7.3 years ago by John David Osborne160
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Fastq Groomer And Compute Quality Statistics
... I noticed that for our new Ilumina data (which generate Sanger format) the FastQ groomer output is identical to the Ilumina FastQ input file. I was hoping to go ahead and just use the raw FastQ files as input (saving disk space) for computing quality statistics to look at box plots, but it appears ...
written 7.3 years ago by John David Osborne160 • updated 7.3 years ago by Tilahun Abebe40

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