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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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File necessary for beta2bam missing #16

Closed rowanhowellGE closed 1 year ago

rowanhowellGE commented 1 year ago

Hi,

I am trying to convert a beta file to a bam using beta2bam. I have setup hg38 as the reference. When i run: wgbstools beta2bed GSM5652219_Oligodendrocytes-Z000000TK.hg38.beta -o GSM5652219_Oligodendrocytes-Z000000TK.hg38.tsv I get the following error:

Invalid input argument
Invalid reference path: /wgbs_tools/references/hg38/CpG.bed.gz

When I look in the "/wgbs_tools/references/hg38" folder, the only entry is hg38.fa.gz. What steps are required to generate the CpG.bed.gz file?

Thanks

yonniejon commented 1 year ago

Hi, did you run the init_genome command?

wgbstools init_genome hg38

This downloads necessary annotation files and creates all other necessary reference files including CpG.bed.gz

rowanhowellGE commented 1 year ago

Hi, I did run init_genome, hence why the hg38.fa.gz file was created. However, looking more closely the init_genome command did raise an error samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory . This was fixed by downloading the libncurses5 package and I now have CpG.bed.gz. Maybe libncurses5 should be added to dependencies?