homer IDR, pseudoreplicates error
Entering edit mode
3.2 years ago
boczniak767 ▴ 830

Hi all,

I'm trying the IDR procedure for FAIRE-seq peaks generated with Homer

The procedure is outlined here homer-idr

It works ok till step 5.

Using command as in example python run_idr.py pseudoreplicate -d [tag_dirs to split] -o [output_file]

I'm getting an error

Creating directory: pseudoreps/individual/hds6-Pseudorep2 and removing existing *.tags.tsv
    Adding tag directory pseudoreps/individual/hds6-Pseudorep2-tmp
    !!! Something is wrong - no reads were added to tag directory !!!
    !!! Check your input files or the makeTagDirectory command options... !!!

I've generated tag directories with command makeTagDirectory hds6 -genome zea_b73 -checkGC ../../MaciekDane/FAIRE_seq/data.fasteris.com/private/HDS/HDS-4-6/hds6passq10.srt.bam -format sam I use custom genome generated from appropriate fasta file.

Above error is generated also by command as in step 6. "Create pseudoreplicates for the pooled directory."

Do you know why I'm getting this error?

Homer FAIRE IDR • 1.0k views

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