User: anna
anna • 10
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- 2 years, 6 months ago
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Posts by anna
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... Thank you so much for your help, i will try it ...
written 7 months ago by
anna • 10
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... Is there any recommended tool to perform Gene Ontology enrichment, but uploading plant protein sequences instead gene ID? ...
written 7 months ago by
anna • 10
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... Thanks a lot! Now i can move forward ...
written 12 months ago by
anna • 10
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... thank you so much for your help! ...
written 12 months ago by
anna • 10
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... I have a lot of rna-seq paired end data which have a very good quality, but some of the files have a lot of overrepresented sequences, not adapters.
I made a blast of these sequences. Some of them didn't match to anything, and some other seems to be rRNA.
I understand that there are divided opinio ...
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Comment:
C: paired end reads cutadapt
... Thanks for your answer. I will consider removing the overrepresented sequences and compare the "clean" data against the raw data, which already have a very good quality of the reads. ...
written 12 months ago by
anna • 10
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5 follow
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... I have several paired end reads files. After performing the FastQC analysis i found out that some pairs have one or more overrepresented sequences. Should i trimm these sequences from both of the two files (1_1 and 1_2)? or just in the only one that have them overrepresented (1_2)?
This is an exampl ...
written 12 months ago by
anna • 10
• updated
12 months ago by
Kevin Blighe ♦ 71k
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... Maybe this is not the appropriate web page for asking this but i don't know where to ask for help.
Does anyone know if there's any software that can help me to reconstruct a proteomics-based metabolic pathway?
In which I can load a data set containing the names of the genes and obtain a model or a g ...
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C: transformed read counts in deseq2
... i've tried that function but the data are not transformed.
Also i've read that the function (rlog) retrieve the transformed counts but i can't get any result by doing this:
write.csv(as.data.frame(rlog(dds, blind=TRUE, fitType = "parametric")), file="transformed.csv") ...
written 19 months ago by
anna • 10
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... How can I extract the normalized and transformed read counts in deseq2 which are used to calculate the log fold change? ...
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20 months ago,
created a question with more than 1,000 views.
For DESeq2 results interpretation
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