COPE is written by Perl. Several Perl modules and other tools are required as followed.
Perl modules:For variants without phase information, we recommend our phasing script which bases on HapCUT and SHAPEIT2.
Unpack the pakeage you have downloaded.
tar -zxvf COPE-TFBS.tar.gz
This will configure serveral paths for different requrements.
You should replace the following paths in cope_tfbs.pl with the real destination in your own system.
my $bedtools_path="/lustre/tools_centos6.3/tools";
Usage:
perl cope_tfbs.pl --variant variant.vcf [--unphased] [--gain]
There should be three subdirectories in your working directory: pwm, resource and script. All PWM files for TFs are stored in the subdirectory named pwm. The annotation resources used by COPE-tfbs are all stored in data subdirectory. Particularly, users should put a fasta file with reference genome sequence named hg19.fa into data subdirectory. The scripts are stored in script subdirectory.
| Flag | Alternate | Description |
|---|---|---|
--variant |
-v |
The VCF must be sorted by chromosome and position. Besides, the VCF file should be put in the |
--unphase |
-u |
This option force COPE to handle variants without phase information. Warning: we don't recommend this option. Default off. |
--gain
|
|
The option is used to decide whether to predict novel TFBS in the whole promoter region. Default off. |
#################################################### # Summary Statistics for TFBS Gain # Number of variants uploaded: 4 # Number of variants creating novel TFBSs: 2 # Number of Novel TFBSs: 1 # Number of multi-variant novel TFBSs: 1 # Number of transcripts affected: 2 #Chr Start End TF Sequence PWM_score Transcript Strand Variant 5 1295224 1295229 ETS_known8 TTTCCG 5.74321215572648 NM_198253(Name=TERT) - 5_1295228_G/A_0|1;5_1295229_G/A_0|1 5 1295224 1295229 ETS_known8 TTTCCG 5.74321215572648 NM_001193376(Name=TERT) - 5_1295228_G/A_0|1;5_1295229_G/A_0|1 #################################################### # Summary Statistics for TFBS Breaking # Number of variants uploaded: 4 # Number of variants within TFBSs: 2 # Number of TFBSs affected: 3 # Number of TFBSs with multi-variants: 2 #Chr Start End TF Ref_PWM_score Alt_PWM_score Strand Nearest_gene Variant 10 100091757 100091764 HIF1A::ARNT_1 6.028847 5.048077 - NM_138469(Name=R3HCC1L;Distance=142243bp) 10_100091761_G/A_0|1 10 100091753 100091766 HIF1A_2 9.043477 7.913043 - NM_138469(Name=R3HCC1L;Distance=142242bp) 10_100091754_G/A_0|1;10_100091761_G/A_0|1 10 100091754 100091765 HIF1A_1 7.916666 6.916666 - NM_138469(Name=R3HCC1L;Distance=142242bp) 10_100091754_G/A_0|1;10_100091761_G/A_0|1
