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Commit 1ee4aa6b authored by jagerfonseca's avatar jagerfonseca
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Update HOMER_Commandlines_SebastaiansData

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#!/bin/bash #!/bin/bash
#Using sebastians output data as my input data. #Skript um Seabstians Output Datn zu testen.
#Not using -opt and -bg paramenter, because in previous try the output remained empty (see wiki request).
#Using the individuell reference genomes. Human and chimpanzee are in HOMER databease, Orangutan RefSeq is downloaded from UCSC. #Using the individuell reference genomes. Human and chimpanzee are in HOMER databease, Orangutan RefSeq is downloaded from UCSC.
Input_Human="/home/jagerfonseca/Input_Sebastian/Human_multi.bed" Input_Human="/home/jagerfonseca/Input_Sebastian/Human_multi.bed"
...@@ -12,16 +10,18 @@ Input_Orang="/home/jagerfonseca/Input_Sebastian/Orang_multi.bed" ...@@ -12,16 +10,18 @@ Input_Orang="/home/jagerfonseca/Input_Sebastian/Orang_multi.bed"
#Using human RefSeq, data are lifted. #Using human RefSeq, data are lifted.
Input_ChimpLIFTED="/home/jagerfonseca/Input_Sebastian/Chimp_multi.humanized.bed" Input_ChimpLIFTED="/home/jagerfonseca/Input_Sebastian/Chimp_multi.humanized.bed"
Input_OrangLIFTED="/home/jagerfonseca/Input_Sebastian/Orang_multi.humanized.bed" Input_OrangLIFTED="/home/jagerfonseca/Input_Sebastian/Orang_multi.humanized.bed"
Input_AllLIFTED="/home/jagerfonseca/Input_Sebastian/All_multi.humanized.bed"
OutputSebastian_Human="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_HUMAN_23.03" OutputSebastian_Human="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_HUMAN_24.03SIZE100.100"
OutputSebastian_Chimp="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_CHIMP_23.03" OutputSebastian_Chimp="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_CHIMP_24.03SIZE100.100"
OutputSebastian_Orang="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_ORANG_23.03" OutputSebastian_Orang="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_ORANG_24.03SIZE100.100"
OutputSebastian_All="/home/jagerfonseca/NO_BACKUP/Output/OutputSebastian_findMotifsGenome_All_24.03SIZE100.100"
#Reference Sequence downloaded from UCSC. #Reference Sequence downloaded from UCSC.
RefSeqOrang="/home/jagerfonseca/GCF_002880775.1_Susie_PABv2_genomic.fna" RefSeqOrang="/home/jagerfonseca/GCF_002880775.1_Susie_PABv2_genomic.fna"
#HOMER/findMotifsGenome.pl with -size 200 (instead 100.100) but with all the other parameters of stephano. Ech line is run with and without normailzation (-noweight). #HOMER/findMotifsGenome.pl with -size 200 (other run with size 100.100) but with all the other parameters of stephano. Each line is run with and without normailzation (-noweight).
#To test data I run them first with len 6,7,8,9 together and noot yet each length on its own. #To test data I run them first with len 6,7,8,9 together and noot yet each length on its own.
findMotifsGenome.pl $Input_Human hg38 ${OutputSebastian_Human}_noweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight findMotifsGenome.pl $Input_Human hg38 ${OutputSebastian_Human}_noweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight
findMotifsGenome.pl $Input_Chimp panTro4 ${OutputSebastian_Chimp}_noweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight findMotifsGenome.pl $Input_Chimp panTro4 ${OutputSebastian_Chimp}_noweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight
...@@ -34,6 +34,8 @@ findMotifsGenome.pl $Input_Orang $RefSeqOrang ${OutputSebastian_Orang} -size 200 ...@@ -34,6 +34,8 @@ findMotifsGenome.pl $Input_Orang $RefSeqOrang ${OutputSebastian_Orang} -size 200
findMotifsGenome.pl $Input_ChimpLIFTED hg38 ${OutputSebastian_Chimp}_LIFTEDnoweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight findMotifsGenome.pl $Input_ChimpLIFTED hg38 ${OutputSebastian_Chimp}_LIFTEDnoweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight
findMotifsGenome.pl $Input_OrangLIFTED hg38 ${OutputSebastian_Orang}_LIFTEDnoweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight findMotifsGenome.pl $Input_OrangLIFTED hg38 ${OutputSebastian_Orang}_LIFTEDnoweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight
findMotifsGenome.pl $Input_AllLIFTED hg38 ${OutputSebastian_All}_LIFTEDnoweight -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 -noweight
findMotifsGenome.pl $Input_ChimpLIFTED hg38 ${OutputSebastian_Chimp}_LIFTED -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 findMotifsGenome.pl $Input_ChimpLIFTED hg38 ${OutputSebastian_Chimp}_LIFTED -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10
findMotifsGenome.pl $Input_OrangLIFTED hg38 ${OutputSebastian_Orang}_LIFTED -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10 findMotifsGenome.pl $Input_OrangLIFTED hg38 ${OutputSebastian_Orang}_LIFTED -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10
\ No newline at end of file findMotifsGenome.pl $Input_AllLIFTED hg38 ${OutputSebastian_All}_LIFTED -size 200 -len 6,7,8,9 -fdr 100 -h -rand -S 10
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