There is a problem with computematrix (and maybe also other tools) when you choose a bedgraph file as an input. Galaxy will let you choose a “bedgraph (as bigwig)” file as an input but will then fail to run and will tell you that your input dataset is in an error state. At first I thought that somet…

Hi @TTP I see both tools at UseGalaxy.org today: One with the option for trimming overhanging coordinates (the version that is best to use after MACS2) → https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ucsc_wigtobigwig/ucsc_wigtobigwig/447+galaxy0 And one with the direct conve…

tools that require bigwig input cannot use bedgraph (as bigwig) file

jennaj Split this topic August 27, 2024, 6:33pm 17

2 posts were split to a new topic: MACS2 bdgcmp troubleshooting

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Bedgraph to Bigwig converter usegalaxy.org support	5	831	September 7, 2022
bigWigToBedGraph: command not found - fatal error 127 usegalaxy.org support galaxy-local	7	1946	July 28, 2020
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Converting bedgraph to bigwig, product files 0 bytes usegalaxy.org support troubleshooting , tool-help , ucsc_wigtobigwig	7	73	December 12, 2024
bedgraph-to-bigwig error usegalaxy.eu support custom-genome , macs2 , chrominfo , custom-build	3	412	November 14, 2023

tools that require bigwig input cannot use bedgraph (as bigwig) file

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