Feed .validPair file into GoTHiC?

[jennymoon90]

Dear nservant, I used to run HICUP2GOTHIC to reform bam file in bowtie_results/bwt2/rawdata to bam.gothic file, and feed into GoTHiC. Recently I encountered a problem with a large database, where in the bam.gothic file "reads were not paired in consecutive rows". I think this is due to presence of invalid pairs in the bam file. Is there a way to convert .validPairs file into a GoTHiC compatible input file? Thank you, Jenny

[nservant]

Hi Jenny, Never look at this point. What is the GoTHiC input format ? I can have a look but not before Septembre. Best

[jennymoon90]

Sure. It’s bam file, or table with columns: chr1 locus1 chr2 locus2. After the input, it will map locus to restriction fragments and calculate frequency of interactions. And then set bins and perform binomial test to output a list of interaction pairs. Thank you, Jenny

Sent from my iPhone

On Aug 14, 2018, at 1:05 AM, Nicolas Servant [email protected] wrote:

Hi Jenny, Never look at this point. What is the GoTHiC input format ? I can have a look but not before Septembre. Best

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