User: Wanderer

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Wanderer10
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8 months, 1 week ago
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1 year, 9 months ago
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Posts by Wanderer

<prev • 18 results • page 1 of 2 • next >
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DESeq2 couldnt run due conflict in annotation
... Hi, I was trying to run DESeq2 but some error is happening: Error in summarizeToGene(txi, tx2gene, ignoreTxVersion, countsFromAbundance) : None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation f ...
deseq2 annotation gtf gene_id transcript_id written 8 months ago by Wanderer10 • updated 8 months ago by Jennifer Hillman Jackson25k
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Comment: C: Cuffdiff analysis output
... Thank you Jen!! Now I am trying another methodology because cummeRbund isnt working yet, anyway thanks!! ...
written 9 months ago by Wanderer10
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Comment: C: Cuffdiff analysis output
... I did the cuffcompare run before running cuffdiff to put p_id and tss_id, the annotation has gene_name, look the output: SQLite Database CDS [30796] CDSCount [61592] CDSData [61592] CDSDiffData [19729] CDSExpDiffData [30796] CDSFeatures [0] CDSReplicateData [61592] TSS [28379] TSSCount [56758] TSSD ...
written 9 months ago by Wanderer10
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Cuffdiff analysis output
... Hi there, I tried to run cuffdiff with the annotation of iGenome but still no sucess to have a output with all statistics results, some results on cuffdiff output are empty @jen any news about the fix of this tool? is there any alternative to cuffdiff working? Thank you! ...
cuffdiff cufflinks rna-seq written 9 months ago by Wanderer10
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Is there an alternative tool to plot RNA-Seq differential expression than cummeRbund?
... I have some results from cuffdiff to plot but I cant use the cummeRbund, is there another tool that can accomplish the same job? I already tried several times to use the cummeRbund but isnt working. Thank you for your time! ...
cuffdiff deseq2 cummerbund plot rna-seq written 10 months ago by Wanderer10 • updated 10 months ago by domi8440
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Galaxy Cuffdiff output doesnt correspont the output from manual
... Hi people! I was trying to run the local version of cummeRbund but the files that I get from the cuffdiff output from galaxy werent the same extension, the manual from cummeRbund says that cuffdiff outputs are those files: isoforms.fpkm_tracking genes.fpkm_tracking cds.fpkm_tracking tss_groups.fpkm ...
cuffdiff galaxy rna-seq written 11 months ago by Wanderer10 • updated 11 months ago by Jennifer Hillman Jackson25k
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Answer: A: how to down load the analysis data from the Galaxy
... You can download all files from your history using the (history options, next to all histories icon) and select the last option ...
written 11 months ago by Wanderer10
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Answer: A: Volcano plot from Tool Shed?
... Try cummerRbund on RNA-SEQ Analysis ...
written 11 months ago by Wanderer10
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Comment: C: Cummerbund isnt working, none of the plots are working
... No problem, the tool worked for print some plots, now I am trying to understand the plots :) Thank you again angel! ...
written 11 months ago by Wanderer10
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Cummerbund isnt working, none of the plots are working
... Hi people, I did the analysis of differential expression with cuffdiff but when I try to plot the results with cummerbund none of plot types are working, what can I do? > Dataset Error An error occured while running the tool toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.1. To ...
cuffdiff cummerbund rna-seq written 11 months ago by Wanderer10 • updated 11 months ago by Jennifer Hillman Jackson25k

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