User: Maciej Jończyk

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Posts by Maciej Jończyk

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Answer: A: Homer getDiffExpression.pl issue
... HI, for me it seems that `getDiffExpression` complains about wrong data type. And indeed, you have negative raw read counts, moreover with strangely added text string eg  "-295,filename5_peak_17638 " I think you should check your bam files, it must strictly meet Homer expectations to be parsed pro ...
written 23 months ago by Maciej Jończyk0
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Answer: A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
... I have the same problem. I have used biomaRt to access gramene data in the past using the default server. Now I'm not able to use it, here is the code:   > listMarts() Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and endi ...
written 3.6 years ago by Maciej Jończyk0
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Comment: C: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
... Or for plants: >listMarts(host="www.gramene.org") ...
written 3.6 years ago by Maciej Jończyk0
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Interpretation of GeneGA results
... Hi All, I'm trying to optimize Streptococcus pyrogenes cas9 sequence (ca. 4000nt) for expression in maize. GeneGA package seems optimal (command GeneGA, optimalizing both codon bias and mRNA secondary structure) but it has poor documentation. I've created custom CAI table. After ca. four days of a ...
genega written 4.6 years ago by Maciej Jończyk0 • updated 4.6 years ago by tomas.bjorklund20

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