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Pre-Requisites
- A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
- Mandatory arguments
- Input alignment folder
- Output folder
- Optional arguments:
- -tbp: maxium tags per bp
- -format: format of the alignment files
- -single: setting this option will place all reads into a single tag file instead of separate tag files for each chromosome
Test with sample data
The following test data are provided for testing BWA-index-mem here /iplant/home/xiaofei_iplant/Sorghum_chr8/chr8_test: (need to update)
- Inputs:
- G3_P_H3_rep1_chr8_Rpe_rmDup.sorted.bam
- G3_P_H3_rep2_chr8_rmDup.sorted.bam
- G3_P_K27me3K4me3_rep1_chr8_rmDup.sorted.bam
- G3_P_K4me3_rep2_chr8_RpermDup.sorted.bam
- -tbp: 1
- -format: BAM
- -single: TRUE
Results
Successful execution of the "makeTagDirectory" will create a directory named "homerTagDir" by default including the tag directory for each alignment input.
Outputs
(need to update)homerTagDir- homerTagDir (test data outputs)
- G3_P_H3_rep1_chr8_R_rmDup_tagDir
- G3_P_H3_rep1_chr8_RpeR_rmDup_tagDir
- G3_P_K27me3K4me3_rep1_chr8Rpe_chr8_R_rmDup_tagDir
- G3_P_K4me3_rep2_chr8_R_rmDup_tagDir