multiple enzymes ligation product

[yinshiyi]

I am trying to analyze data that uses multiple REs. I learned that from ARIMA kit: ^GATC,G^ANTC ligation product of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC

What should these digest_genome.py -r G^ANTC ^GATC C^TNAG T^TAA -o bed.bed Fasta.fa Restriction site(s) GAATC,GACTC,GAGTC,GATTC,GATC,CTAAG,CTCAG,CTGAG,CTTAG,TTAA Offset(s) 1,1,1,1,0,1,1,1,1,1

What should my ligation product be? Thank you.

[yinshiyi]

--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

[yinshiyi]

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