User: k.witmer

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k.witmer10
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1 year, 8 months ago
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k*******@imperial.ac.uk

Posts by k.witmer

<prev • 10 results • page 1 of 1 • next >
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Comment: C: RNA STAR "empty"
... Thanks Jen! Will use HiSat2 for now, but wanted to try STAR as I am interested in antisense reads... ...
written 10 months ago by k.witmer10
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Comment: C: RNA STAR "empty"
... Hi Jen, I tried on useGalaxy.org again with adjusted input datasets, but have the same outcome...i.e. the output is empty. Would you have any more suggestions please? ...
written 10 months ago by k.witmer10
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Comment: C: RNA STAR "empty"
... Hi Jen, thanks for your help. The custom genome is not large, it is 18Mb. I sorted it according to chromosomes (14 chromosomes, 2 mitochondrial genomes and some contigs), but I just saw that the gff file is slightly differently sorted, do you think this could be a problem? I am working at usegalaxy ...
written 10 months ago by k.witmer10
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RNA STAR "empty"
... Hi there, I wanted to run RNA STAR to align my RNAseq data. The genome I am working on is not in the directory, but I added a genome fasta file as well as a gff3 file when running the program. however, it somehow doesn't finish with the analysis. This is what I get in Galaxy: Oct 10 11:19:33 ..... ...
galaxy rna-seq written 10 months ago by k.witmer10 • updated 10 months ago by Jennifer Hillman Jackson25k
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Comment: C: normalisation between different ChIP-seq data
... Hi, yes I have been using these tools to get a better idea of the distribution of the mark and how it correlates with already published transcriptional data. The end goal would be to get a list of genes that are enriched in H3K9ac for each condition/stage. Enrichment in terms of 5UTR, ORF, or 3UTR ...
written 14 months ago by k.witmer10
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normalisation between different ChIP-seq data
... Hi there, I guess it is a recurrent problem, but I haven't found a satisfying answer yet. I have 4 ChIP-seq datasets looking at H3K9ac coverage, each from a different life cycle stage (or different conditions I guess, with the difference that there is not really a "non-treated" or wt sample). I woul ...
chip-seq h3k9ac macs2 normalisation written 14 months ago by k.witmer10
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jobs paused due to "The previously selected dataset has entered an unusable state"
... Hi there, i just reported an error (through usegalaxy) but I got additional information I would like to share. My jobs are paused and I cannot get them unpaused. The reason is then given as follows: "The previously selected dataset has entered an unusable state". when having a closer look, this prev ...
unusable state jobs paused written 15 months ago by k.witmer10 • updated 15 months ago by Jennifer Hillman Jackson25k
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Comment: C: Job delays at http://usegalaxy.org (all including upload)
... Glad it was an easy problem, too! thanks Jen! ...
written 15 months ago by k.witmer10
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Comment: A: file does not load
... Hi thanks! I am working with http://usegalaxy.org ...
written 15 months ago by k.witmer10
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Job delays at http://usegalaxy.org (all including upload)
... Hi there, I wanted to load a gff file into Galaxy, but the job is waiting to run for hours now. I tried with another gff file, same result. I deleted the file and reloaded it, still nothing happens. Can you please let me know what is going on? I checked on twitter but didn't see anything announced. ...
dataset delay usegalaxy.org job upload written 15 months ago by k.witmer10 • updated 14 months ago by Jennifer Hillman Jackson25k

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