User: fana

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fana0
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Posts by fana

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caret RFE - ordinal outcome
... I am using R package caret to develop predictive models. Could I use rfe function (recursive feature elimination) when I have an ordinal outcome (eg. cancer stage)? ...
recursive feature elimination machine learning written 5 months ago by fana0
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STAR aligner options for unstranded RNA-seq
... I plan to do STAR-htseq using an unstranded RNA-seq dataset. I can only find in the manual that the option --outSAMstrandField intronMotif is needed for cufflinks only. It's not clear to me if I need to specify that option or any other option specific for unstranded data in order to use other quanti ...
alignment next-gen rna-seq star aligner written 9 months ago by fana0 • updated 9 months ago by Devon Ryan91k
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MiRNA orthologues between human and chick
... I am trying to find miRNA ortholgues between human and chick. Is it valid to say that the ones with exactly the same name are ortholgues? For example, hsa-let-7a-2-3p and gga-let-7a-2-3p. ...
orthologues microrna mirna written 2.2 years ago by fana0 • updated 24 months ago by Biostar ♦♦ 20
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Comment: C: miRDeep2.pl error when reads.fa input file contains info for more than one sampl
... Thank you for the example. Could you please have a quick look at my commands? I did collapse reads (see the top lines of the 'reads.fa' file below too). I expect that when you have multiple samples some sequences might be the same across them. mapper.pl config.txt -d -e -p galGal4 -s processed_ ...
written 2.3 years ago by fana0 • updated 7 months ago by h.mon26k
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Comment: C: mirdeep2: miRDeep.pl error
... Have you solved this problem? ...
written 2.3 years ago by fana0
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miRDeep2.pl error when reads.fa input file contains info for more than one sample
... Hi, I am having trouble using miRDeep2 package. It looks like I am running mapper.pl using a config.txt file which contains multiple samples correctly. However, when I try to run miRDeep2.pl I get the following error. If I run quantifer.pl it runs smoothly though. Any ideas? Error: problem wit ...
next-gen mirna-seq mirdeep2 written 2.3 years ago by fana0 • updated 7 months ago by h.mon26k

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Popular Question 5 months ago, created a question with more than 1,000 views. For miRDeep2.pl error when reads.fa input file contains info for more than one sample

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