Shiyi Yin

i think so, failed for me too

thanks

activate: No such file or directory i tested i can use conda activate bds_atac but source activate bds_atac failed

i think i solved it, i replace the if ( conda_env != "" ) conda_py2 = \ "if [[ -f $(which $conda_bin_dir"+"conda) && $($conda_bin_dir"+"conda env list | grep $conda_env |...

PCR Duplicates: 20,614,012 (7.93%) Optical Duplicates: 890,663 (0.34%) These looks fine. Inter-chromosomal: 1,320,146 (0.51% / 0.93%) Intra-chromosomal: 7,458,303 (2.87% / 5.27%) Short Range (20Kb): 2,886,831 (1.11% / 2.04%) These looks...

--restriction_site 'G^ANTC ^GATC C^TNAG T^TAA' \ --ligation_site 'ANTCGANT,ANTCGATC,ANTCCTNA,ANTCTTA,GATCGANT,GATCGATC,GATCCTNA,GATCTTA,TNAGGANT,TNAGGATC,TNAGCTNA,TNAGTTA,TAAGANT,TAAGATC,TAACTNA,TAATTA' \ I attached my ideas, will update on results

 The pipeline failed at mapped_2hic_fragments.py -f fragment.bed -r sa22224_S3HiC_R.5_bwt2pairs.bam --all no validated pairs are detected

I am glad there is someone else in the same boat. I am by no means expert, I am also trying to figure this out. Here is what I found....

 ######################################################################### ## Data ######################################################################### PAIR1_EXT = muscle_R1 PAIR2_EXT = muscle_R2 what is your folder structure? here is what mine look like

PAIR1_EXT = 4DNEXC8P1KZ6_R1 PAIR2_EXT = 4DNEXC8P1KZ6_R2 maybe try this?