User: zhalford

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zhalford0
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Posts by zhalford

<prev • 5 results • page 1 of 1 • next >
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BAM tool?? tab-delimited, coordinate sorted output file - displays calls, depth at every coordinate?
... I'm trying to figure out how to create a tab-delimited, coordinate sorted, file type that displays the depth at each coordinate included in the .bed file. What file can I start with and what tools, if possible, can I use to modify to get the intended result I need? ...
bam samtools written 4 weeks ago by zhalford0 • updated 28 days ago by Jennifer Hillman Jackson25k
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Comment: A: Uploading local files to create valid datasets for analyses
... That isn't even the right file type i'm looking for. I'm trying to figure out how to create a tab-delimited, coordinate sorted, file type that displays the depth at each coordinate included in the .bed file. What file can I start with and what tools, if possible, can I use to modify to get the int ...
written 4 weeks ago by zhalford0
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Comment: A: Uploading local files to create valid datasets for analyses
... Hey, so I'm trying to basically use galaxy to unzip my gVCF.gz files -- i guess by uploading them and "converting" them to VCF files... The issue is, I only have the option to covert it to tabix. Even if I wanted to use the VCFtoTab-delimited tool, I cannot - it requires VCF. What should I do? ...
written 4 weeks ago by zhalford0
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IT PGM File type - every base position total coverage + alt allele coverage
... Hey everyone, To simplify my question: -I've sequenced a single sample Is there an Ion Torrent-PGM file type, that is excel compatible, that will at least express the total coverage and alt allele coverage (and maybe other QC metrics) of every aligned base position (in the .bed)? I'd like it to b ...
file type coverage metrics assembly written 5 weeks ago by zhalford0
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Uploading local files to create valid datasets for analyses
... Hi, so very new to this... I have tried a number of different file types to upload - the tools of analysis that I'd like to use all have said "no dataset available." What do I need to do differently to get these files once sucessfully uploaded, "available"? ...
galaxy upload written 7 weeks ago by zhalford0

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