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Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Mandatory arguments 
    1. Input alignment folder
    2. Output folder
  3. Optional arguments:
    1. -tbp: maxium tags per bp
    2. -format: format of the alignment files
    3. -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)

  1. Inputs:
    1. G3_P_H3_rep1_chr8_Rpe_rmDup.sorted.bam
    2. G3_P_H3_rep2_chr8_rmDup.sorted.bam
    3. G3_P_K27me3K4me3_rep1_chr8_rmDup.sorted.bam
    4. G3_P_K4me3_rep2_chr8_RpermDup.sorted.bam
    Note: These are outputs of Picard_MarkDup-2.7.0.
  2. -tbp: 1
  3. -format: BAM
  4. -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

  1. homerTagDir (test data outputs)
    1. G3_P_H3_rep1_chr8_R_rmDup_tagDir
    2. G3_P_H3_rep1_chr8_RpeR_rmDup_tagDir
    3. G3_P_K27me3K4me3_rep1_chr8Rpe_chr8_R_rmDup_tagDir
    4. G3_P_K4me3_rep2_chr8_R_rmDup_tagDir