create_cisTarget_databases
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Published
20 hours ago •
aertslab
aertslab
Can the input motifs be in the PWM format?
Hi, can the input motifs be in the PWM format? Like outputs from HOMER program (motif1.motif), an example please check bellow:
>TGCATG 1-TGCATG,BestGuess:hsa-miR-4262 MIMAT0016894 Homo sapiens miR-4262 Targets (miRBase)(0.647) 5.179177 -34261.033795 0 T:22354.0(48.77%),B:2355.3(5.54%),P:1e-14879
0.001 0.044 0.001 0.954
0.001 0.001 0.997 0.001
0.001 0.997 0.001 0.001
0.997 0.001 0.001 0.001
0.001 0.001 0.001 0.997
0.001 0.001 0.997 0.001
Best,
Keren
The motifs need to be in Cluster-Buster format.
The following function will create them (put one homer motif per file).
homer_to_clusterbuster () {
local homer_motif_file="${1}";
awk -F '\t' -v 'OFS=\t' '{ if ($1 ~ />/) { print $1 } else if (NF == 4) { print $1 * 100, $2 * 100, $3 * 100, $4 * 100; } }' "${homer_motif_file}";
}
$ cat /tmp/motif.homer
>TGCATG 1-TGCATG,BestGuess:hsa-miR-4262 MIMAT0016894 Homo sapiens miR-4262 Targets (miRBase)(0.647) 5.179177 -34261.033795 0 T:22354.0(48.77%),B:2355.3(5.54%),P:1e-14879
0.001 0.044 0.001 0.954
0.001 0.001 0.997 0.001
0.001 0.997 0.001 0.001
0.997 0.001 0.001 0.001
0.001 0.001 0.001 0.997
0.001 0.001 0.997 0.001
$ homer_to_clusterbuster /tmp/motif.homer
>TGCATG
0.1 4.4 0.1 95.4
0.1 0.1 99.7 0.1
0.1 99.7 0.1 0.1
99.7 0.1 0.1 0.1
0.1 0.1 0.1 99.7
0.1 0.1 99.7 0.1
The motifs need to be in Cluster-Buster format.
The following function will create them (put one homer motif per file).
homer_to_clusterbuster () { local homer_motif_file="${1}"; awk -F '\t' -v 'OFS=\t' '{ if ($1 ~ />/) { print $1 } else if (NF == 4) { print $1 * 100, $2 * 100, $3 * 100, $4 * 100; } }' "${homer_motif_file}"; }$ cat /tmp/motif.homer >TGCATG 1-TGCATG,BestGuess:hsa-miR-4262 MIMAT0016894 Homo sapiens miR-4262 Targets (miRBase)(0.647) 5.179177 -34261.033795 0 T:22354.0(48.77%),B:2355.3(5.54%),P:1e-14879 0.001 0.044 0.001 0.954 0.001 0.001 0.997 0.001 0.001 0.997 0.001 0.001 0.997 0.001 0.001 0.001 0.001 0.001 0.001 0.997 0.001 0.001 0.997 0.001 $ homer_to_clusterbuster /tmp/motif.homer >TGCATG 0.1 4.4 0.1 95.4 0.1 0.1 99.7 0.1 0.1 99.7 0.1 0.1 99.7 0.1 0.1 0.1 0.1 0.1 0.1 99.7 0.1 0.1 99.7 0.1
Thank you for your explaination!
Best,
Keren
Our SCENIC+ public motif collection is now available: https://resources.aertslab.org/cistarget/motif_collections/