User: jm.keith

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jm.keith60
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Posts by jm.keith

<prev • 9 results • page 1 of 1 • next >
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Answer: A: start with BAM file
... Also, I recommend searching the forum for your topic before posting. If it's already been asked/answered before, chances are likely that your posts will be ignored. Example- [https://biostar.usegalaxy.org/p/20545/][1] [1]: https://biostar.usegalaxy.org/p/20545/ ...
written 8 months ago by jm.keith60
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Answer: A: BED to BAM tool error
... Hello to both, Thanks for the assist. I tried to rerun with the correct genome file (thanks), but I still get the same error. This file is a bed file of filtered reads that I'm trying to use to build a heatmap. Thus the reason I can't use the original BAM file. Any other suggestions are appre ...
written 8 months ago by jm.keith60
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Answer: A: start with BAM file
... No, that's not correct. The first line of the page tells you: "Please note the updated server to use for FTP: usegalaxy.org. This replaces the prior server "main.g2.bx.psu" in all materials below." **http://usegalaxy.org**, for Galaxy Main Also, I recommend checking out the video on that page. ...
written 8 months ago by jm.keith60
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BED to BAM tool error
... Hi, I'm trying to convert from BED to BAM using Galaxy, but though the tool runs fine, I get an error which makes the file unusable. I am using sorted BED files. First 6 lines of my bed file: Chrom Start End Name Score Strand chr1 12634845 12634885 ...
bam bedtools written 8 months ago by jm.keith60
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Answer: A: start with BAM file
... You need to use an FTP to transfer large files to Galaxy. https://wiki.galaxyproject.org/FTPUpload ...
written 8 months ago by jm.keith60
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Answer: A: FASTAQ not able to be selected in BWA, though FastaQC passed
... You may need to run your files through the FastQGroomer tool to put them into the correct format ...
written 10 months ago by jm.keith60
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Problems with MACS peak calling--FDRs of 100%
... Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (input, p300, H3K4me, H3K27Ac and a TF file)--for the histone modification and TF files, I am able to call peaks nicely with in-range FDR%. With the p300 files, however, I am unable to call peaks without F ...
chip-seq macs galaxy peak calling written 10 months ago by jm.keith60
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Answer: A: About CHIP Seq Data Download
... Start with reading and exploring the Geosets Database https://www.ncbi.nlm.nih.gov/gds ...
written 11 months ago by jm.keith60
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Answer: A: I'm having trouble running the MACS function in Galaxy
... Sorry, slight mistake in the above inquiry. My genome size is 1.87e9 ...
written 12 months ago by jm.keith60

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