Arima HiC ligation motif

[KatrinPla]

Hi, I have a short question concerning the Arima kit: according to https://nf-co.re/hic/docs/usage the following is stated: --restriction_site ARIMA kit: ^GATC,^GANT

--ligation_site '[Ligation motif]' Exemple of the ARIMA kit: GATCGATC,GATCGANT,GANTGATC,GANTGANT

However, on the Arima webpage they say: "The Arima-HiC chemistry uses restriction enzymes that digest chromatin at ^GATC and G^ANTC, where N can be any of the 4 genomic bases. Our multiple restriction enzyme chemistry produces the following possible ligation junction motifs: GATCGATC, GANTGATC, GANTANTC, GATCANTC."

I am wondering where the difference comes from. I'd appreciate if you could help me with that!

Best, Katrin

[nservant]

Dear Katrin Yes, sorry, there is a mistake in the doc. It should be fixed soon with the ongoing PR. It should be "ARIMA kit: ^GATC,G^ANTC" and "Exemple of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC". Best Nicolas

[KatrinPla]

Dear Nicolas, thanks a lot for your fast response! I am less confused now :)

Best, Katrin

On 14.06.2020, at 21:16, Nicolas Servant notifications@github.com wrote:

Dear Katrin Yes, sorry, there is a mistake in the doc. It should be fixed soon with the ongoing PR. It should be "ARIMA kit: ^GATC,G^ANTC" and "Exemple of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC". Best Nicolas

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[cemmeydan]

FYI, it looks like the config is still not matching the Arima documentation (G^ANT instead of G^ANTC, plus the corresponding ligation motifs). Was that intentional?

'arima' {
       restriction_site='^GATC,G^ANT'
       ligation_site='GATCGATC,GATCGANT,GANTGATC,GANTGANT'
    }