User: virlana.shchuka

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Posts by virlana.shchuka

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Comment: C: MACS2 input not recognized by tool
... Hi Jennifer, Thanks for your quick reply. The issue is that when I upload the bedgraph files, the bdgbroadcall "MACS score in bedgraph" section says "no bedgraph dataset available". The files I'm uploading are definitely bedgraph files, so I don't think it's a format issue. Does the MACS tool need ...
written 14 months ago by virlana.shchuka0
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MACS2 input not recognized by tool
... Hi all, I've been using Galaxy to analyze my ChIP-seq data, and have managed to get the program to call narrow peaks when I uploaded my bam files. I want to call broad peaks as well though, and the bedgraph files I upload onto the Galaxy disk are not being recognized by the MACS2 bdgbroadcall progr ...
chip-seq macs2 datatype metadata input written 14 months ago by virlana.shchuka0 • updated 14 months ago by Jennifer Hillman Jackson23k
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Input: gene name (UCSC-style) Desired output: promoter sequences in FASTA format
... Hi everyone! I have a list of 450 gene names for which I need to find the promoter sequences (I will later use a program to find the TF motifs in said promoter sequences). I have very little experience with bioinformatics and programming, and was wondering what is/are the most interface-friendly pr ...
galaxy extract promoter ucsc fasta written 14 months ago by virlana.shchuka0 • updated 14 months ago by Jennifer Hillman Jackson23k
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Getting Genome Coordinates for a List of ENSEMBL IDs
... I need to convert a list of ENSEMBL IDs from an RNA-seq dataset to UCSC mm9 genome coordinates. Any suggestions as to how to go about it? ...
reference-genome ucsc identifiers ensembl written 14 months ago by virlana.shchuka0 • updated 14 months ago by Jennifer Hillman Jackson23k

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