User: iraia.munoa

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iraia.munoa60
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Posts by iraia.munoa

<prev • 28 results • page 1 of 3 • next >
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Comment: C: CPM plot for individual genes
... Well thanks!!! I will try! ...
written 5 weeks ago by iraia.munoa60
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Comment: C: CPM plot for individual genes
... Well I have been reading the link you showed me, but I am a little bite confused and don't understand what I need to run in `edgeR`. In the coments James Ashmore provides a cpm.DGEList function, do I need to run it like that? Or running `cpm(y, log=TRUE, lib.size=libsize, prior.count=2)` after the ` ...
written 5 weeks ago by iraia.munoa60 • updated 5 weeks ago by ATpoint18k
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Comment: C: output TMM normalized counts with edgeR
... ...
written 5 weeks ago by iraia.munoa60
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CPM plot for individual genes
... Hi! I am working with my DEGs list from `edgeR` with TMM normalization. I have seen in many publications that researches plot `log2(FPKM)` values for individual DEGs to show the statistical significance. Regarding this, I would like to know if it is posible to plot the `log2(CPM)` values of contro ...
cpm rna-seq edger tmm written 5 weeks ago by iraia.munoa60 • updated 5 weeks ago by ATpoint18k
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Association database between repetitive elements and ncRNAs
... Hi everybody, Is there a database with validated associations between repetitive elements and ncRNAs? I mean specifying interaction or regulation between repetitive elements and ncRNAs? Can someone help me? Thanks !! Iraia ...
ncrnas lncrnas repetitive elements mirnas written 11 weeks ago by iraia.munoa60
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Comment: A: Oligo: GeneChip miRNA 4.0 analysis only returns control probes
... Hi! I am in the same point. Is it posible when doing the rma() for normalization to obtain more columns added in the output file, I mean other information apart from the ID name of the miRNA, such as the specie, transcript ID, etc. Or the only way to know this info is to take the output and do an i ...
written 12 weeks ago by iraia.munoa60
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Comment: C: Problems with the reference genome in Stringtie
... Well, when doing the mapping with your file and then stringtie with the lincRNA annotation file, the warning disapears. But, if I look to the output of stringtie, I only see the name of the genes of the lincRNA annotation file. And my question, which maybe cames from some fault on understanding th ...
written 3 months ago by iraia.munoa60
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Comment: C: Problems with the reference genome in Stringtie
... Thanks Devon for your answerd, So this is the general reference genome? The last option in gencode werb page?(Genome sequence, primary assembly (GRCm38), Nucleotide sequence of the GRCm38 primary genome assembly (chromosomes and scaffolds)) This one? I use the lncRNA reference genome described in th ...
written 3 months ago by iraia.munoa60
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Problems with the reference genome in Stringtie
... Hi everybody! I am using RNA-Seq protocol for identifying differentially expressed lncRNAs. I have used the reference genome from gencode: gencode.vM20.lncRNA_transcripts.fa I have build the index and then run hisat2: > hisat2 --dta -q -x mm10_lncRNA_genome -U C-P1_28454_ACAGTG_trimmed.fq.gz ...
stringtie reference genome rna-seq lncrna written 3 months ago by iraia.munoa60 • updated 3 months ago by Devon Ryan90k
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Comment: C: Not clustered terms in david ontology functional annotation clustering
... Ok, thanks Kevin. It was more a thing of understanding correctly the way David works, as I did not find anything about it in their manual. Thanks!! ...
written 3 months ago by iraia.munoa60

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Student 5 months ago, asked a question with at least 3 up-votes. For How to see if adjusting batch effect in RNA-seq is working or not

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