waveform_pipeline

Look for waveform files with given start, end and bed information.

1. to identify the waveform stp files with given start, end and bed information output: list target waveform files paths in the output csv file output1.csv with the following columns: bed, start, end, isExist, path, start_stp, end_stp

2. to check coverage of the waveform files with given bed information output: a list of waveform files with the given bed information and the coverage information output: a list of waveform files with the given bed information and the coverage information in the output csv file output2.csv with the following columns: bed, start, end, isExist, path, start_stp, end_stp, coverage(%)

3. download output: actual stp files in folder output3_stp_files

4. process the stps with https://github.com/hulab-ucsf/wftools output: stp files that in adbin format, also trimmed and aligned to the requested bed information in the input csv file output: actual adibin files in folder output4_adibin_files