User: mc2548

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mc254810
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Posts by mc2548

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Finding non-regulatory regions genome wide for TF-binding ananlysis
... I have ATAC-seq reads genome wide and my next step is to look for enriched motifs or TF-binding motifs in these regions. As control I was planning on using non-open regions in the genome. Is there any way to extract the non-coding regions in the genome which does not have ATAC peaks but is of same ...
genome sequencing written 4 weeks ago by mc254810
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Comment: C: Making chain files
... As you pointed out, I have been having trouble to install the parasol job submission system. This is where I downloaded it from: https://genecats.gi.ucsc.edu/eng/parasol.html but this does not look like what is described in here: http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system . Any ...
written 5 weeks ago by mc254810
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Comment: C: Making chain files
... From my understanding, this is for 2 different assemblies for the same reference genome/organism. How different will it be for 2 distant species? ...
written 5 weeks ago by mc254810
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Making chain files
... I work on non-model insect genomes. In order to look for orthologous regions across species I have had been blasting in the past. But I needed something more robust. I used the online version of mVista and that has been helpful but was recently advised to use liftover. Realised that I needed chain f ...
genome assembly alignment sequence written 5 weeks ago by mc254810 • updated 29 days ago by Biostar ♦♦ 20
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Comment: A: Paired end peak callers
... For paired end reads, specially ATAC-seq, you can use fseq: http://fureylab.web.unc.edu/software/fseq/ ...
written 11 weeks ago by mc254810

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