User: sergio.espeso-gil

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3 years ago
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Post-doctoral Fellow

Icahn School of Medicine at Mount Sinai

 


 

Posts by sergio.espeso-gil

<prev • 54 results • page 1 of 6 • next >
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Answer: A: Extracting non-interacting hic reads to create a sam/bam file
... Thanks! That was really useful actually! :-)   ...
written 3 months ago by sergio.espeso-gil0
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Extracting non-interacting hic reads to create a sam/bam file
... Hi! I would like to extract the not chimeric reads from hic data and create a bam file with it. I have been trying, but with not much success. I saw that maybe with DiffHic could be feasible (currently checking) or with HiCPro that generates a sam file with the chimeric reads (I need to know how to ...
diffhic hic hicpro written 3 months ago by sergio.espeso-gil0
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Comment: C: Subsampling bam file - error DiffBind
... Thanks!!! That´s was the error, now working fine! I could not live without youuuuuuuu and Rory hahaha  THANKS!!!    ...
written 7 months ago by sergio.espeso-gil0
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Subsampling bam file - error DiffBind
... Hi community! I am subsampling input control data for DiffBind analysis to test something. I have merged first input files by using samtools merge and then later samtools view -s "percentage of subsampling"   When I am trying to run DiffBind, then I get this error: 'subsampled_input.bam'  does n ...
diffbind samtools written 7 months ago by sergio.espeso-gil0 • updated 7 months ago by Gord Brown560
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Comment: C: Providing specific regions to Diffbind
... Thanks Rory   ...
written 10 months ago by sergio.espeso-gil0
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Providing specific regions to Diffbind
... Hi community! I am providing to Diffbind a genomic region list to be analyzed (not peaks, just regions of interest). Although the results are good, I want to avoid Diffbind to merge some of the regions that actually overlap. Can I do that? I have trying so far with no success. Any help?   Thanks! ...
chipseq diffbind written 12 months ago by sergio.espeso-gil0 • updated 12 months ago by Rory Stark2.1k
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Comment: C: CSAW: getBestTest p-value
... Ok, I see. For whatever reason I though that they could also sort by significance, but in fact they both report a p-value per cluster following different strategies. To sort by significance I need to do section 7.2, rigth?  ...
written 2.2 years ago by sergio.espeso-gil0
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CSAW: getBestTest p-value
... Hi Aaron,  Sorry for being so annoying asking questions, at the end I have decided that predefined regions is not worth it by now (at least), maybe at the future. I have arrived to a good filtering normalisation options for my ChIPs (I think), and I am just merging and getting the windows with stro ...
csaw written 2.2 years ago by sergio.espeso-gil0 • updated 2.2 years ago by Gordon Smyth32k
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Comment: C: CSAW: Annotation through clustering with external information
... Ok, thanks Aaron. I will try. What I also need to ask you is how to enter my own predefined regions, I guess I need to read GRanges documentation, right?  Have a nice day ...
written 2.2 years ago by sergio.espeso-gil0
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Answer: A: CSAW: Annotation through clustering with external information
... Hi Aaron for the answers. Concerning my second question: tabpromoter is setted as follows: olap<- findOverlaps(promoter, rowRanges(filtered)) olap tabpromoter<- combineOverlaps(olap, results.promoter$table) head(tabpromoter[!is.na(tabpromoter$PValue),]) Concerning the error: > test_up ...
written 2.2 years ago by sergio.espeso-gil0 • updated 2.2 years ago by Gordon Smyth32k

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