User: anna

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anna10
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Posts by anna

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Comment: C: GO enrichment through protein sequences
... Thank you so much for your help, i will try it ...
written 7 months ago by anna10
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GO enrichment through protein sequences
... Is there any recommended tool to perform Gene Ontology enrichment, but uploading plant protein sequences instead gene ID? ...
enrichment sequences tool go proteomic written 7 months ago by anna10
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Comment: C: removing overrepresented sequences from rna-seq
... Thanks a lot! Now i can move forward ...
written 12 months ago by anna10
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Comment: C: removing overrepresented sequences from rna-seq
... thank you so much for your help! ...
written 12 months ago by anna10
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removing overrepresented sequences from rna-seq
... 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 ...
trimmomatic overrepresented sequences cutadapt written 12 months ago by anna10 • updated 12 months ago by h.mon32k
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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 anna10
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paired end reads cutadapt
... 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 ...
overrepresented sequences cutadapt written 12 months ago by anna10 • updated 12 months ago by Kevin Blighe71k
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Software to reconstruct a proteomics-based metabolic pathway
... 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 ...
software proteomics metabolic pathway written 15 months ago by anna10 • updated 15 months ago by gabt110
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Comment: 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 anna10
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transformed read counts in deseq2
... How can I extract the normalized and transformed read counts in deseq2 which are used to calculate the log fold change? ...
data deseq2 read counts written 19 months ago by anna10 • updated 19 months ago by Prakash2.1k

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Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 results interpretation

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