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License: GNU General Public License v3.0
A processing guide for IMPLICON data (bisulfite amplicon data for imprinted loci)
License: GNU General Public License v3.0
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!
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