Can GISTIC 2.0 be run on CCLE_segment_cn.csv 2021Q4 directly?

Q&A
,
1

Hi. I want to run GISTIC2 on the CCLE_segment_cn.csv version 2021Q4 to get a region-level data of each cell line. I have some questions.
First, I dont know if this segment file can be used for GISTIC2 analysis since it seems the Segment_Mean column (values of which are positive) is somewhat different from the Segment_Mean column (containing both positive and negative values) of the standard segment file.
Second, according to the GISTIC2 manual, a markers file is optional. I wonder how I can get the markers file or if I can run the GISTIC2 with default paramter.
Third, I have run GISTIC2 using resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta and an error was reported:
Number of columns on line 2 of ASCII file /media/md2/BAB4C270B4C22EA7/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta must be the same as previous lines.
I wonder if I could use the UCSC hg38 fasta file.
Finally, is there any code example about gistic2 of CCLE data?
Thanks.

2

Can anyone else answer the question?

3

Hi. You can use this link to construct your marker file. Our segment files are 2^MEAN_LOG2_COPY_RATIO (more info here), so you’d need to apply a log2 transform to the data. Unfortunately we currently do not have a code to share. You can find the reference genome information here. -best