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zsq-berry / 3D-genome-tools

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Converting txt to .hic #2

Open Oksanak22 opened 1 year ago

Oksanak22 commented 1 year ago

Thank you for the script, but I have some issues with converting homer.txt.gz to .hic. I tried to run java -Xmx4g -jar juicer_tools.jar pre -r 20000 -d /home/juicebox/GSM_20000_homer.txt.gz Lib2.hic Tb.fasta and it gave me an error:

java.io.IOException: Unexpected column count. Check file format at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:148) at juicebox.tools.utils.original.AsciiPairIterator.(AsciiPairIterator.java:72) at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:555) at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:669) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:419) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:122) at juicebox.tools.HiCTools.main(HiCTools.java:94) java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment. at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1772) at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1541) at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:954) at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:671) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:419) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:122) at juicebox.tools.HiCTools.main(HiCTools.java:94)

Actually, I am able to open GSM_20000_homer.txt with Treeview but I need to have a .hic file for downstream analysis

Could you, please help me with that?

Thank you.