User: mosharrofgeb

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Posts by mosharrofgeb

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Comment: C: DEseq normalization Small RNA-seq data using rRNA
...   Well, thank you very much for your patience and time. Initially I used normal DESeq pipeline. But I noticed that there were enrichments for ribosomal RNA expression in my experimental library. The reason is: probably as the rRNA are pretty abundant in my libraries (both my control and exp), as th ...
written 2.9 years ago by mosharrofgeb0
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Comment: A: DEseq normalization Small RNA-seq data using rRNA
... Well, here is what I want: My control library has 400 million reads whereas my experimental library has ~5 million reads. So, the normal R studio usage is: normalize both libraries by their relative depth (what I have understood) and use that factor for normalizing different loci (their expression) ...
written 2.9 years ago by mosharrofgeb0
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Comment: A: DEseq normalization Small RNA-seq data using rRNA
...   I am not an expert on R. I just need to get my things done! Probably I am not using the commands in the right way......I used these commands below (I have 4 untreated (un) replicates, 2 treated (t) replicates), sorry for all these silly questions: > countdata <- read.table("Dcr2.txt", hea ...
written 2.9 years ago by mosharrofgeb0
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Comment: C: DEseq normalization Small RNA-seq data using rRNA
... I have just started. So, I think I can use DEseq2 then. But still, I need solution for my problem! ...
written 2.9 years ago by mosharrofgeb0
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Comment: C: DEseq normalization Small RNA-seq data using rRNA
... Well, I am actually using DEseq. Not DEseq2. Do you think I should use DEseq2 instead of Deseq? Thanks.     ...
written 2.9 years ago by mosharrofgeb0
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DEseq normalization Small RNA-seq data using rRNA
...     Hello: I am using DEseq2 for Small RNA-seq data. I have four replicates for control and two replicates for treated. I want to see differential expression of different kinds of loci (like expression of all gypsy elements in control vs treated). But I want to normalize my two datasets using All  ...
smallrna normalization deseq2 ribosomal rna written 2.9 years ago by mosharrofgeb0

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