Hi,
I'm trying to use PeakSeq v1.1 to call peaks on Illumina reads. I used the preprocess option to process both my Input and Experiment sam files. I downloaded the mappability file of hg19 (my reads were mapped to chr1-22, X, Y, and M) from Gernstein Lab's website. But when I run the peak_select option, I get a segmentation fault in the middle. When I rerun, it stops at exactly the same place. I have 6 different experiment files, and they all behave the same way, although the place at which they give the error is different from one another. I thought it may have something to do with the input, so I tried using the -validate_fragments. But I don't understand what am I to do with its output. I don't know what is giving this error, and any help is really appreciated. Here is my config.dat file:
Experiment_id N2UO_Peaks
chromosome_list_file hg19_chr_list
Enrichment_fragment_length 200
target_FDR 0.05
N_Simulations 10
Minimum_interpeak_distance 200
Mappability_map_file mappability_hg19.txt
ChIP_Seq_reads_data_dirs SO_2365_N2UO_Bound
Input_reads_data_dirs SO_2365_INPUT_pooled
Simulation_seed 1234567
Background_model Simulated
max_Qvalue 0.05
Let me know if any other info is needed.
Thanks a lot,
TEJ
EDIT: Figured out the reason. The chrM reads were somehow creating an issue. When I reran without chrM in the list, there were no issues
I'm trying to use PeakSeq v1.1 to call peaks on Illumina reads. I used the preprocess option to process both my Input and Experiment sam files. I downloaded the mappability file of hg19 (my reads were mapped to chr1-22, X, Y, and M) from Gernstein Lab's website. But when I run the peak_select option, I get a segmentation fault in the middle. When I rerun, it stops at exactly the same place. I have 6 different experiment files, and they all behave the same way, although the place at which they give the error is different from one another. I thought it may have something to do with the input, so I tried using the -validate_fragments. But I don't understand what am I to do with its output. I don't know what is giving this error, and any help is really appreciated. Here is my config.dat file:
Experiment_id N2UO_Peaks
chromosome_list_file hg19_chr_list
Enrichment_fragment_length 200
target_FDR 0.05
N_Simulations 10
Minimum_interpeak_distance 200
Mappability_map_file mappability_hg19.txt
ChIP_Seq_reads_data_dirs SO_2365_N2UO_Bound
Input_reads_data_dirs SO_2365_INPUT_pooled
Simulation_seed 1234567
Background_model Simulated
max_Qvalue 0.05
Let me know if any other info is needed.
Thanks a lot,
TEJ
EDIT: Figured out the reason. The chrM reads were somehow creating an issue. When I reran without chrM in the list, there were no issues
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