Entering edit mode
8.3 years ago
Chirag Nepal
★
2.4k
Hi all,
I analyzed CNV in the population using GISTIC2 and have expected result.
Now, I would like to extract the gene count (reoccurring count) and associated q-value for that gene.
I tried to dig the standard output text file from GISTIC
wc -l *txt
23110 all_data_by_genes.txt
223 all_lesions.conf_75.txt
23110 all_thresholded.by_genes.txt
1152 amp_genes.conf_75.txt
23110 broad_data_by_genes.txt
41 broad_significance_results.txt
41 broad_values_by_arm.txt
1152 del_genes.conf_75.txt
23110 focal_data_by_genes.txt
17 sample_cutoffs.txt
16 sample_seg_counts.txt
Can somebody please point out the files (perhaps combination of files) from where I could extract information.
If anybody have experience this, please share.
Thanks!