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fangwuwang / team_Bloodies

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Homer Findingmotifs TFBS #15

Open fangwuwang opened 7 years ago

fangwuwang commented 7 years ago

@rawnakhoque I asked the PDF in our lab and he showed me that everything has been done in bash. Follow the installation and basic configuration step by step here. As shown in the webpage, genome configuration is done using this line (see Download Homer Packages session)-- perl /path-to-homer/configureHomer.pl -install hg19_ And to do the analysis there is only one line to run (link)-- findMotifsGenome.pl <peak/BED file> -size # [options]

acavalla commented 7 years ago

Hi all! Just uploaded all the knownResults files into the dna meth folder. Rawnak, I'm not sure why we would have got different results. I used -size given -mask -preparse

rawnakhoque commented 7 years ago

I think we need the de novo results file not the known results.

On Sun, Apr 2, 2017 at 8:32 PM, acavalla notifications@github.com wrote:

Hi all! Just uploaded all the knownResults files into the dna meth folder. Rawnak, I'm not sure why we would have got different results. I used -size given -mask -preparse

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acavalla commented 7 years ago

We discussed this when we met and decided to go with the known. What is the benefit of the others in our analysis?

rawnakhoque commented 7 years ago

@acavalla Can you please upload all the text files for known motifs? These files should be in your output folder when you completed the jobs.

acavalla commented 7 years ago

@rawnakhoque done :)

rawnakhoque commented 7 years ago

@acavalla Thanks! :)