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[utterances-bot]

bedGraphToBigWig manual with usage examples | BioQueue Encyclopedia

bedGraphToBigWig - Convert a bedGraph file to bigWig format.. BioQueue Encyclopedia provides details on the parameters, options, and curated usage examples for bedGraphToBigWig.

https://open.bioqueue.org/home/knowledge/showKnowledge/sig/ucsc-bedgraphtobigwig

[hzauyangxin]

I input ’bedGraphToBigWig sample.sorted.bedGraph $fai(download by fetchChromSizes) sample.bw' ,but zhe output file is empty when I use 'bigWigInfo sample.bw'. my bedGraph like this : chr1 9650 9650 100.000000
chr1 9853 9853 100.000000
chr1 15504 15504 100.000000
chr1 22410 22410 0.000000 and my result of bigWigInfo llike this: version: 4
isCompressed: yes
isSwapped: 0
primaryDataSize: 20,403,285
primaryIndexSize: 153,252
zoomLevels: 10
chromCount: 557
basesCovered: 0
mean: -nan
min: 0.000000
max: 100.000000
std: -nan

[bioq-comm]

BedGraph track data values can be integer or real, positive or negative values. The chromosome coordinates are zero-based, half-open. When you set identical chromStart and chromEnd, you're creating a feature of length 0. So applying -1 to the second column should solve the problem.

[hzauyangxin]

Thank you for the insightful explanation. I now understand that when the chromStart and chromEnd values are identical, it creates a feature of length 0, which causes issues. Applying -1 to the second column to adjust the chromEnd value is a great solution to ensure that the intervals are valid and non-zero length. I appreciate the helpful guidance, and it definitely resolved the issue.