User: k.witmer

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k.witmer10
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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 5 weeks 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 5 weeks 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 5 weeks 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 6 weeks ago by k.witmer10 • updated 5 weeks ago by Jennifer Hillman Jackson23k
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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 6 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 6 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 6 months ago by k.witmer10 • updated 6 months ago by Jennifer Hillman Jackson23k
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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 6 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 6 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 6 months ago by k.witmer10 • updated 6 months ago by Jennifer Hillman Jackson23k

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