segment sites mismatch - Githubissues

nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

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segment sites mismatch #64

Closed chang-bwl closed 1 month ago

chang-bwl commented 8 months ago

Hello, I tried to split the beta (hg19) of the cell_WGBS in the paper : $ wgbstools segment --betas *beta --min_cpg 3 --max_bp 2000 -o blocks.small.bed

The following error occurred： [wt beta] WARNING: beta file size (28,587,300 sites) incomatible with current genome reference (28,217,448 sites) Invalid input argument [wt segment] ERROR: current genome reference (hg19) does not match the input beta file (GSM5652208_Coronary-Artery-Smooth-Muscle-Z00000420.beta).

How can I solve it? Thanks

chang-bwl commented 7 months ago

I've finally solved this problem.It's because wget -c downloads have some extra lines in the download file, which causes the CSI to lag