GEMS error regarding chr19

Question

[Mohit]

Hello everybody!!

I am running the GEMS for the Peak calling. as input I am giving the sam file and

Command:

java -Xmx4G -jar /home/admin1/software/gems/gem/gem.jar \
  --d /home/admin1/software/gems/Read_Distribution_ChIP-exo.txt \
  --g /home/admin1/software/gems/hg19.info \
  --genome /home/admin1/software/gems/hg19.info \
  --expt /home/admin1/data/chipexo/srr346/SRR346403.sam \
  --f SAM \
  --out CTCF_Human \
  --k_min 13 \
  --k_max 13

output:

Events discovered
Significant:    67573
Insignificant:    4810
Filtered:    32

Total 32109 homotypic events (within 500bp of other events).
Finish binding event prediction: 2.1m
Refine read distribution from 2000 binding events.
Loading genome sequences ...
chr19.fa file is not found at /home/admin1/software/gems/hg19.info.

Why this chr19.fasta file is not found error is there ..??

[Sukhi Singh]

What is in the file /home/admin1/software/gems/hg19.info

[Mohit]

This file contains information like:

1       249250621
10      135534747
11      135006516
11_gl000202_random      40103
12      133851895
13      115169878
14      107349540
15      102531392
16      90354753
17      81195210
17_ctg5_hap1    1680828
17_gl000203_random      37498
17_gl000204_random      81310
17_gl000205_random      174588
17_gl000206_random      41001
18      78077248
18_gl000207_random      4262
19      59128983
19_gl000208_random      92689
19_gl000209_random      159169
1_gl000191_random       106433
1_gl000192_random       547496
2       243199373

and so on..

I don't know what is this information

Answer 1

[Yuchun Guo]

--genome should be the genome sequences (see here).

BTW, the name of the method is GEM.