User: p.barnett

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p.barnett50
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Posts by p.barnett

<prev • 10 results • page 1 of 1 • next >
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Comment: C: All jobs I submitted yesterday are labeled as "Job is waiting to run"
... Yep, having the same problem with merging BAM files. Server also seemed slow last week ...
written 25 days ago by p.barnett50
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Answer: A: Featurecounts on Galaxy main
... Hi Jen, Thanks for your help, again. After checking the output again I spotted (though why I didn't earlier) that those lacking counts had double registries in the GTF. So when I permitted multiple feature assignment of the same read.... hey presto! Phil ...
written 4 months ago by p.barnett50
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Featurecounts on Galaxy main
... I have a general question/issue I wonder if anyone knows a solution to. Firstly, as I said in a previous message, i was pleased with the integration of built-in annotation files (mm10, Hg19 etc) in featureCounts on Galaxy main. I am now analyzing Rat genome data (rn6 build). The data looks good on c ...
counts annotation featurecounts rna-seq written 4 months ago by p.barnett50
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Answer: A: Recent problems writing Bigwig from Bam files
... OK, fixed my problem. The issue was that the STAR file used for mapping just used chromosome number and not chr(n). So I manually renamed the chromosomes in this file and remapped using STAR. I still need to sort my BAM once I have uploaded it to the Galaxy main, but the BigWig looks fine. Thanks f ...
written 4 months ago by p.barnett50
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Answer: A: Recent problems writing Bigwig from Bam files
... Yes, I'm working on the main galaxy server. I'm guessing the problem lies in the genome I'm using, Rat rn6. I get good mapping on STAR and the features_count function can count it on the main server with no problems using a GTF of rn6. I can also see the BAM file reads if I display it at UCSC...... ...
written 4 months ago by p.barnett50
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Recent problems writing Bigwig from Bam files
... I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A few weeks ago this wasn't an issue, though had to name sort my Bam file first. Now the file fails, regardless if I sort, don't sort or sort coordinates. Any solutions ? ...
bam bigwig galaxy star convert written 4 months ago by p.barnett50
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Featurecounts' added built-in annotations
... Not a question: Just to say thanks for adding the 'built-in' annotation files under featureCounts. This has vastly improved the counting I was doing with imported GTF based files from UCSC ...
rna-seq gene annotation alignment featurecounts written 6 months ago by p.barnett50 • updated 6 months ago by Jennifer Hillman Jackson25k
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Problems running Deseq2 jobs
... For the past 24 hours I have been trying to run DEseq2 jobs on the main server (usegalaxy.org), but with no success (message reads, 'there is no package getopt'). Other jobs, such as features count, have successfully run. Server status says ok, I also tried rerunning jobs that ran fine 2 days ago, b ...
galaxy deseq2 usegalaxy.org rna-seq error written 8 months ago by p.barnett50 • updated 8 months ago by Jennifer Hillman Jackson25k
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Answer: A: Queueing issues on usegalaxy.org
... Issues seem resolved this morning.... Thanks ...
written 20 months ago by p.barnett50
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Queueing issues on usegalaxy.org
... I seem to be having some issues with queueing uploaded files this morning (CET). Uploaded files sometimes enter the queue quickly and others take forever. Reentering the jobs that havent queued works occasionally, but then not always. Jobs that do eventually start are random in the list with no posi ...
galaxy written 20 months ago by p.barnett50

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