Trying to use Wig/BedGraph-to-bigWig tool for a file generated with mapping to CHM13 T2T but the bedgraph file I am trying to convert does not allow me to designate the reference genome as CHM13 T2T (it does not come up on the list).

[image] TTP: RuntimeError: Invalid interval bounds! This part of the error indicates a mismatch between the chromosomes + coordinates between the two inputs. Double check that all are based on the exact same reference genome assembly/build. You have mentioned both hg38 and CHM13_T2T_v2.0 – s…

Welcome, @TTP The tool Wig/BedGraph-to-bigWig interprets the assigned database metadata of the input file. This is true for any input for this tool. If no database is assigned, the tool will not recognize any input datasets (a built-in quality check). If you mapped in Galaxy, the output should hav…

Thanks. Yes, mapping works fine with BWA-MEM and the correct genome is shown. I run RMDUP on this and the genome also shows fine. But when the files go into MACS2, the bedgraph files that are generated show a “unspecified” database/build. When I try to put in the genome to fix this, the T2T build is…

Thank you for sharing more details. I also see that my last queue job finished and failed in my test history. An index file is missing! That probably explains all the problems. /cvmfs/data.galaxyproject.org/managed/len/ucsc/CHM13_T2T_v2.0.len We will need to fix this. Thank you so much for follow…

Great - thanks for helping with this. Just so I am clear though, if the bedgraphs were derived from CHM13 data but then specified as hg38 then the repeat information is there or not there?

Hi @TTP Update! We were able to create the missing index for the CHM13_T2T_v2.0 assembly. My rerun job of the failed test was successful. You should also rerun, starting from the first step that lost the database assignment (MACS2?). We will be creating a brand new set of indexes for the hs1 assem…

Thanks; I am re-running these. I have a question about a failed multibigwigsummary run. Is this also having to do with a CHM13 issue? The error shows this: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/lib/python3.8/multiprocessing/pool.py", line 1…

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CHM13 T2T genome not found in options for some tools

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mapping, macs2, custom-genome, igv, custom-build

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