User: maria

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maria10
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Posts by maria

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Tximport and pseudo alignment with Kallisto
... Hi there, I am using Kallisto to generate counts in my RNA-seq experiments. Since in the downstream analysis I am preferring DESeq2, I have to use tximport for importing transcript abundances in order to perform differential expression analysis. I am slavishly following the code used in the tximpor ...
deseq2 tximport kallisto written 10 days ago by maria10 • updated 10 days ago by Michael Love23k
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adapter trimming paired vs unpaired reads
... I have been practising with Trimmomatic for days but it is still not clear to me whether or not the paired output reads (in a pair-ended sequencing) are the ones needed for the downstream alignment. kind regards, Maria. ...
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DESeq2, how to deal with batch effect: t-test or design matrix?
... Hello, generally speaking, when we are dealing with human tissues dataset (different hospitals, different days, etc.) we have to take into account the so-called batch effect. I have been practising with some useful tool such as SVA package but someone else like to cope with this issue in a slightly ...
sva deseq2 design matrix batch t-test written 21 days ago by maria10 • updated 21 days ago by Michael Love23k
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Comment: C: tximport, Kallisto and Deseq2 (quick answer)
... That's sounds great, thanks a lot either for this support and for giving me the opportunity to do good science thanks to your packages. ...
written 29 days ago by maria10
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Comment: C: tximport, Kallisto and Deseq2 (quick answer)
... Thanks a lot for your quick reply. So, just for clarity sake, that may be one of the possible solution: txi.kallisto.tsv <- tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreTxVersion = TRUE) sampleTable <- data.frame(condition = factor(c("a","a","a","b","b","b")) rown ...
written 29 days ago by maria10
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tximport, Kallisto and Deseq2 (quick answer)
... Hello there, I am trying to analyse a dataset using deseq2 with kallisto via tximport. I am using the following code: tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreTxVersion = TRUE) So, in this case the counts from abundances are 'no', I guess (because I am not specifying so It should ...
deseq2 counts tximport kallisto written 4 weeks ago by maria10 • updated 29 days ago by Michael Love23k

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