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Shians / NanoMethViz

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nanopolish input format #21

Closed yinshiyi closed 8 months ago

yinshiyi commented 1 year ago

######################### it seems the input is sample chr pos strand statistic read_name

nanopolish has the output chromosome strand start end read_name log_lik_ratio log_lik_methylated log_lik_unmethylated num_calling_strands num_motifs sequence 1 + 136533276 136533276 86bbfb92-5a22-44f7-aa58-e61d6ea3cd48 1.34 -165.98 -167.32 1 1 TGAGCCGTTTG 1 + 136533377 136533377 86bbfb92-5a22-44f7-aa58-e61d6ea3cd48 0.34 -214.55 -214.89 1 1 AGACTCGGGGA 1 + 136533400 136533400 86bbfb92-5a22-44f7-aa58-e61d6ea3cd48 -10.52 -251.71 -241.18 1 1 GAGGGCGATGG

this stat column is log_lik_ratio column?

Thank you

Shians commented 1 year ago

Hi there, it sounds like you are trying to use NanoMethViz directly with the output of Nanopolish. You need to import it into the NanoMethViz format first using create_tabix_file().

BeatrizFaustino commented 1 year ago

how to transform nanopolish output to nanomethviz?