User: jlzheng

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jlzheng0
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Posts by jlzheng

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cuffmerge error report
... Fatal error: Error running cuffmerge: [Tue Jul 3 08:52:11 2018] Beginning transcriptome assembly merge ------------------------------------------- [Tue Jul 3 08:52:11 2018] Preparing output location cm_output/ [Tue Jul 3 08:52:31 2018] Converting GTF files to SAM [08:52:31] Loading reference a ...
cuffmerge written 5 weeks ago by jlzheng0
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Answer: A: Featurecounts built-in annotation hg38, hg19, mm10, mm9
... Thanks Jen! I have solved the problem and proceeding to the next! ...
written 10 weeks ago by jlzheng0
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Featurecounts built-in annotation hg38, hg19, mm10, mm9
... "Parameter genome requires a value, but has no legal values defined" stop me from execution. which I typed "mm10" in the blank box. How can I type in to give the matched annotation of mm10 I want to use? ...
galaxy featurecounts annotation built-in written 11 weeks ago by jlzheng0
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RNA-seq result after cuffdiff with no significance.
... I analysed samples(two replicates for each group) with overexpression of my interest, I find that overexpression is successful compared from OE to control, but all q_value comes out from cuffdiff are higher than 0.05 and shows no significance including the overexpression gene. which FPKM differs fro ...
cuffdiff p-value q-value fpkm test written 6 months ago by jlzheng0 • updated 6 months ago by Jennifer Hillman Jackson25k
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The giant different FPKM value of same gene between cufflink and cuffdiff.
... It differs a lot (10 times as large) between cufflink outputs "gene_FPKM tracking" and cuffdiff outputs"gene differential expression testing". Is it normal in such results? ...
cuffdiff expression fpkm cufflinks rna-seq written 6 months ago by jlzheng0 • updated 6 months ago by Jennifer Hillman Jackson25k

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