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Rocky Parida
Dec 28, 2016, 1:34:12 PM12/28/16
to MEME Suite Q&A
Hi All
I am using an input sequence set to generate motifs using MEME. My background file contains all the upstream sequences I found for all the genes in the genome minus my input sequence set.
Next, I using the motif matrices generated from MEME to scan across my input sequence set to get all the significant occurrences of the motifs (generated by MEME) using FIMO. In my FIMO analysis I am also using the same background file as above. Now, I am trying to find significant occurrences of the same motifs (generated by MEME) in an entirely different second input sequence set. I am wondering if I can do a background file in one of the two following ways:
a) background file contains all the upstream sequences I found for all the genes in the genome minus my second input sequence set.
b) background file contains all the upstream sequences I found for all the genes in the genome minus (my second input sequence set+my first input sequence set).
Any suggestion or comment is highly appreciated.
Rocky
I am using an input sequence set to generate motifs using MEME. My background file contains all the upstream sequences I found for all the genes in the genome minus my input sequence set.
Next, I using the motif matrices generated from MEME to scan across my input sequence set to get all the significant occurrences of the motifs (generated by MEME) using FIMO. In my FIMO analysis I am also using the same background file as above. Now, I am trying to find significant occurrences of the same motifs (generated by MEME) in an entirely different second input sequence set. I am wondering if I can do a background file in one of the two following ways:
a) background file contains all the upstream sequences I found for all the genes in the genome minus my second input sequence set.
b) background file contains all the upstream sequences I found for all the genes in the genome minus (my second input sequence set+my first input sequence set).
Any suggestion or comment is highly appreciated.
Rocky
Rocky Parida
Dec 29, 2016, 2:50:02 PM12/29/16
to MEME Suite Q&A
Hi All
I tried both option a) and b) backgrounds and got same results. So, in a way I conclude it is irrelevant to pick one over the other for my analysis.
Thanking you
Rocky
I tried both option a) and b) backgrounds and got same results. So, in a way I conclude it is irrelevant to pick one over the other for my analysis.
Thanking you
Rocky
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