User: jfo

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jfo20
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3 years, 11 months ago
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Posts by jfo

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Batch correction in DESeq2
... Hello Kevin, I am one of the confused ones regarding removing batch effects. How is 'accounted for' different from 'removal'? When is it correct to use the 'accounted for' (i.e. using the ~batch+cond formula) approach and when is it correct for removal of the batch effect? Thank you for shedding li ...
written 16 days ago by jfo20
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Comment: C: Removing UniVec sequences in Assembly
... This worked. I used k=21. I am not sure why. But, thanks.... ...
written 16 days ago by jfo20
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Removing UniVec sequences in Assembly
... My first time uploading my de novo transcriptome assembly to TSA. I got flagged with Code(VECTOR_MATCH). I tried to trim the vector using bbduk and cutadapt, but I couldn't seem to make it work. For example, this adapter: >gnl|uv|NGB00150.1:1-46 Ambion FirstChoice RLM-RACE 3' RACE adapter ...
assembly tsa bbduk rna-seq cutadapt written 20 days ago by jfo20 • updated 17 days ago by genomax85k
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Comment: C: Differential gene expression analysis by DESeq2
... This also cleared up my confusion. But, at the same time, led me to another one: which method is more useful? I am under the impression that we the "right" way of doing it is to to test significance of expression vs 0, hence I would be inclined to use method B. I am not sure when to use the method A ...
written 3 months ago by jfo20
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Answer: C: Could not shrink after adjusting factor level reference in DESeq2
... Sorry about that. The error shows up because of the factor levels (changed reference to latik from keme) and the lfcShrink needs the right value for the coef (which can be determined using resultsName). The correct value would be the original keme as reference, i.e., condition_keme_vs_latik. To ...
written 3 months ago by jfo20 • updated 3 months ago by ATpoint36k
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Comment: C: Could not shrink after adjusting factor level reference in DESeq2
... Okay. Sorry. I found a link to "Note on factor levels". Silly me. ...
written 3 months ago by jfo20
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Could not shrink after adjusting factor level reference in DESeq2
... my two conditions are Keme and Latik, so I have condition_keme_vs_latik (based on dds). I want Latik to be the reference so: res <- results(dds, lfcThreshold = lfc_cutoff, alpha = padj_cutoff, contrast = c("condition", "latik", "keme") Now, to shrink the LFC: resLFC <- lfcShrink(dd ...
deseq2 rna-seq lfcshrink written 3 months ago by jfo20
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GO annotation on diamond blasted transcriptome (nr db)
... Hello! So far, Approaches to GO annotation of transcriptomes of non-model organisms (besides B2G) point to the use of Trinotate and Genescf. I would like to ask if there is an easy way to directly add GO annotation to a diamond blast result (against NCBI nr)? Since B2G is really slow on a basic sub ...
diamond go blast rna-seq written 6 months ago by jfo20
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Comment: C: GeneBank accession 2 Entrez gene id
... Hi! How do we use this for accessions representing multiple organisms, especially non-model ones? for example: XP_021371371.1 and PIK53657.1 ...
written 6 months ago by jfo20
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Comment: C: Kissplice2reftranscriptome error : IndexError
... Thank you Vincent! Everything went smoothly now. :) ...
written 11 months ago by jfo20

Latest awards to jfo

Scholar 3 months ago, created an answer that has been accepted. For C: Could not shrink after adjusting factor level reference in DESeq2
Popular Question 16 months ago, created a question with more than 1,000 views. For Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)
Popular Question 17 months ago, created a question with more than 1,000 views. For Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)

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