User: lessismore

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lessismore930
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Posts by lessismore

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Comment: C: Filter for nonoverlapping genomic hits and keep the longest one
... Congrats <3 That's a great solution! ...
written 4 days ago by lessismore930
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Filter for nonoverlapping genomic hits and keep the longest one
... Dear all, i'm dealing with genomic coordinates of TF binding site mapping and i would like to filter the huge FIMO output for the non-overlapping sites. For each overlapping site i would like to keep the longest hit. Is there a way or a package to do this in R ? here i attach an example of my data: ...
genomic ranges genomics filtering written 5 days ago by lessismore930 • updated 4 days ago by rpolicastro3.2k
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Comment: C: Filtering the result of transcription factor binding matrix prediction from PWM
... Hi! How was the experience with FIMO ? I am curious about * how did you selected the window for FIMO? e.g. 1-2-5Kb or >5Kb regions for promoters? I am using RSAT-tools for that * which parameters did you set (1e-4 for p-value i think is a bit low, i am considering to select 1e-4 for q-valu ...
written 10 days ago by lessismore930
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Difference between "Original tree" and "Bootstrap consensus tree" in Mega X software for phylogeny
... Dear all, i've used a multiple sequence alignment to generate a phylogenetic tree on Mega X software with maximum parsimony method (500 bootstrap replicates). The result of this analysis is, as for Mega X visualization, a window named "Original tree" and another one names "Bootstrap consensus tree" ...
phylogeny mega written 9 weeks ago by lessismore930
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Comment: C: Revive old microarray data linking it to new gene annotations
... Thanks, this is actually super useful. ...
written 3 months ago by lessismore930
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Comment: C: Revive old microarray data linking it to new gene annotations
... Thank you, lll have a look at this. I was referring to GeneChip/DNA Chip ...
written 3 months ago by lessismore930
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Revive old microarray data linking it to new gene annotations
... Dear all, i'm dealing with a plant species with old microarray experiments from before 2010. As i want to integrate this data with new data corresponding to annotations from its brand new genome, what do you recommend to do? A simple best-blast-hit against the new transcript file would do the job? I ...
annotations integration microarray written 3 months ago by lessismore930
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Comment: C: Download entire gene sequences (including UTRs) with BioMart-Ensembl
... I'm looking for the entire gene sequences as for my purpose i want information on UTRs and introns. Thats why i chose that option. ...
written 3 months ago by lessismore930
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Comment: C: Download entire gene sequences (including UTRs) with BioMart-Ensembl
... Thank you. Could you tell if this annotation is normally done by genome paper authors or by the Ensembl staff? I don't think i've ever read, at least in plant papers, about UTR annotation pipeline. ...
written 3 months ago by lessismore930
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Download entire gene sequences (including UTRs) with BioMart-Ensembl
... Dear all, I want to download gene sequences for a list of genes, including UTR annotations. I was for some reason sure that this information was provided for each genome at the moment of release coming from some gene model identification step. I was thus sure to have extracted also the UTR regions ...
ensembl genomes utr written 3 months ago by lessismore930

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