Hi all,
First time poster here. I had a question regarding the program PScan.
I recently tried downloading all matrices from Jaspar and giving that list to Pscan (as I didn't want to limit myself to one model organism, PScan does). Unfortunately I received an error message :
Matrix with invalid name found! (only letters and digits allowed).Custom Matrices Error.
I was wondering if anyone had any advice on how to rectify these matrices to make them work in PScan ?
My current matrices look like this:
>MA0001.2 AGL3
A [22 16 25 27 0 0 82 40 56 35 65 25 64 0 33 52 45 21 ]
C [29 9 8 16 92 79 1 4 0 0 1 4 0 0 14 5 23 24 ]
G [34 29 4 13 0 0 2 3 1 0 4 3 28 92 15 7 13 26 ]
T [10 41 58 39 3 16 10 48 38 60 25 63 3 3 33 31 14 24 ]
Thanks!
•
written
by
naren.srinivasan •
According to the help page: http://159.149.160.51/pscan/help.html#Input you are very close:
>matrix1
A_1 A_2 ..... A_n
C_1 C_2 ..... C_n
G_1 G_2 ..... G_n
T_1 T_2 ..... T_n
>matrix2
A_1 A_2 ..... A_n
C_1 C_2 ..... C_n
G_1 G_2 ..... G_n
T_1 T_2 ..... T_n
You should be able to remove the A,C,T,G,[,], characters, you may have to remove the gene name too. Try it on a couple of matrices first.
E.g.
>MA0001.2
22 16 25 27 0 0 82 40 56 35 65 25 64 0 33 52 45 21
29 9 8 16 92 79 1 4 0 0 1 4 0 0 14 5 23 24
34 29 4 13 0 0 2 3 1 0 4 3 28 92 15 7 13 26
10 41 58 39 3 16 10 48 38 60 25 63 3 3 33 31 14 24
Thanks!
Is there a way to do this en mass for all the transcription factors in the list without going through each one manually?
•
written
by
naren.srinivasan •
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