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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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Any detailed description of the input files for summarizeModifications softwares #100

Open Jingquan-Li opened 7 months ago

Jingquan-Li commented 7 months ago

Hi, I have ran the ipdsummary and got the base modification GFF file. Then I want to use summarizeModifications softs for summarizing kinetic DNA modifications. But I read the SMRT link manual, I only find the informations of input file 'alignmentSummary ' option for "coverage summary GFF generated by resequencing pipelines". Would you tell the details for how to generate the "coverage summary GFF" or where could get an example file.

Thanks, Jingquan.

anjatolic commented 3 months ago

Hi, I had the same question and managed to figure it out. You can use cromwell.workflows.pb_align_ccs workflow for the alignment to a reference and this will produce coverage GFF that is needed forsummarizeModifications, together with modification GFF (form ipdSummary). The other option to get these files is from Microbial Genome Analysis workflow cromwell.workflows.pb_microbial_analysis. Hope this helps!