How to generate a BED file with the list of restriction fragments after digestion

[Takeshi]

Hi Nicolas,

I want to generate a BED file with the list of restriction fragments for a less specific enzyme, Eco47I (AvaII).

Its recognition site is G^GWCC (W=A or T). 

In this case, can I use a command line for double digestion 

as cited in https://github.com/nservant/HiC-Pro/blob/master/doc/UTILS.rst

digest_genome.py -r G^GACC G^GTCC -o mm9_hindiii_dpnii.bed mm9.fasta

Sincerely, 

Takeshi

[nservant]

Yes, it should work.
If you want to double check, you can load the BED output file in the UCSC genome browser and compare your fragments with the restriction enzyme track. 
Hope it helps
N

[Takeshi]

Hi Nicolas,

Thank you for your response.
I could generate the bed file.

In the config-hicpro.txt file,
can I describe two ligation sites as follows ?:

GENOME_FRAGMENT = AvaII_resfrag_mm9.bed
LIGATION_SITE = GGACC
LIGATION_SITE = GGTCC


Best,

Takeshi





2016年8月1日月曜日 16時43分23秒 UTC+9 nservant:

[nservant]

Hi Takeshi,
Sorry for the delay
In theroy, you can use ;
LIGATION_SITE = GGACC,GGTCC

I think it should work. But honnestly, I never use it that way.
If you do that I think that checking in details the results of the mapping should be a good idea. Especially, at the end of the bowtie2 step1, when it generates the list of unmapped reads and then tries to trim them based on the ligation motif.
If you find something weird, please let me know so that I could investigate this in details.
Nicolas

[Takeshi]

Hi Nicolas, 

Thank you for your kindness.

I will try it.

Takeshi

2016年8月5日金曜日 0時35分06秒 UTC+9 nservant:

[Michael Kaufman]

Did specifying multiple ligation sites in this way work for you?