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…

CHM13 T2T genome not found in options for some tools

usegalaxy.org support

jennaj Split this topic July 20, 2023, 10:14pm 10

2 posts were split to a new topic: SAM BAM conversion and sort order

Topic		Replies	Views
Converting bedgraph to bigwig, product files 0 bytes usegalaxy.org support troubleshooting , tool-help , ucsc_wigtobigwig	7	85	December 12, 2024
bedgraph-to-bigwig error usegalaxy.eu support custom-genome , macs2 , chrominfo , custom-build	3	418	November 14, 2023
ATAC Seq wig to bigwig transformation of MACS2 data usegalaxy.org support workflow , tool-help	6	29	June 9, 2025
Custom genome help and troubleshooting plus where to find HISAT2 alignment statistics custom-genome , custom-build	5	1667	October 31, 2019
FTDNA BAM to T2T pileup and haplogroup usegalaxy.org.au support workflow , variant-analysis	2	223	May 7, 2024

CHM13 T2T genome not found in options for some tools

Related topics