felixkrueger / implicon Goto Github PK

Hi Felix,

I download a few samples from the implication paper (mouse non allelic specific) and I manage to reproduce all the steps in your pipeline, except for the last one. This command:

./filter_coordinates_mouse_not_allele_specific.py CpG_imprinted_positions_mouse.txt

generates a empty file (only with the header).

I running the script inside the folder containing the outputs from the deduplication step, and the script identifies all the files:
'CpG_OT_SRR11207804.sra_1_8bp_UMI_R1_val_1_bismark_bt2_pe.deduplicated.sam.gz.txt.gz', 'CpG_OB_SRR11207802.sra_1_8bp_UMI_R1_val_1_bismark_bt2_pe.deduplicated.sam.gz.txt.gz',
(...)

but then the methylation_state_consistency.txt is empty

any ideas what the problem might be?

thanks a lot in advance!