User: José Luis Lavín

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Posts by José Luis Lavín

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Comment: C: Annotation files for bacterial genome RNAseq
... Hello again, I finally managed to "correct" the gff file enough as to get rid of the duplications on it (I never thought this format could be such a pain, maybe its inexperience with it, but it took me hours to correct the errors) and generate the TranscriptDB from it . But now I get some warnings ...
written 5.4 years ago by José Luis Lavín80
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Comment: C: Annotation files for bacterial genome RNAseq
... Dear Jim, I've tried your recommendation, and it worked on the main bacterial genome gff, I'm finding problems with plasmid .gff files, while trying to join the gff from the 2 plasmids of the organism. Since the gff are from prokaryotic origin, no exon feature is included in this plasmids gff, so I ...
written 5.4 years ago by José Luis Lavín80
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Comment: C: Annotation files for bacterial genome RNAseq
... Thank you very much to the list and specially to all those who answered my question. I'm a little overwhelmed with all this tsumani of information right now, but I expect to be able to use it in a short time. I will test those solutions you offered me and try to determine which is the best for me a ...
written 5.4 years ago by José Luis Lavín80
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Answer: A: Annotation files for bacterial genome RNAseq
... First of all I want to thank Michael for his swift answer. Then I have a concern about this, Am I wrong or the package "easyRNASeq" is dramatically lacking an update at its bioconductor page. I mean that manual script and vignette are not up to date (at least R complains when I try to use functions ...
written 5.4 years ago by José Luis Lavín80
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Annotation files for bacterial genome RNAseq
... Dear list members, I have to analyze bacterial transcriptomic data and I have a doubt about how to proceed. I have downloaded the reference genome FASTA from the NCBI and also a gff file containing the annotation of that reference. I can map the reads to the genome and so on, but when the time com ...
alignment annotation assign written 5.4 years ago by José Luis Lavín80 • updated 5.4 years ago by James W. MacDonald51k
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Answer: A: ChIPpeakAnno "examplePattern.fa" file
... Dear Julie & Paul, Please excuse my delay answering you back. Thank you very much for your help with this issue, I'll read the rGADEM vignette to try it in my analysis. Best wishes JL 2013/3/1 Paul Shannon > I offer below a short example of using rGADEM with MotifDb which you may > f ...
written 6.7 years ago by José Luis Lavín80
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Comment: C: ChIPpeakAnno "examplePattern.fa" file
... Thank you Julie, I misunderstood the functionality and thought I was a "de novo" motif finder... Any insight on how to predict motifs from ChIPseq experiments? Any R module that does it and you can recommend? May you think of implementing this function to your awesome package? ;) JL 2013/2/27 Zhu ...
written 6.7 years ago by José Luis Lavín80
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ChIPpeakAnno "examplePattern.fa" file
... When looking for motif occurrence in the peaks, the "examplePattern.fa" file you supply with the module: -Is a standard example pattern file you can use for any set under analysis or is it a custom one you include in the package referred to a particular set of motifs? -May you give a hint on how t ...
written 6.7 years ago by José Luis Lavín80 • updated 6.7 years ago by Julie Zhu4.1k

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