CEAS giving strange graphical output when supplying --gn-groups

[jereeder]

I'm trying to run CEAS on two different sets of genes that are present in my ChIP-seq, but it seems as though I'm doing something incorrectly. When I run CEAS without the --gn-groups parameter, I get great results. I see reasonable looking profiles in the wiggle section of the .pdf output.

However, when I run CEAS with the --gn-groups parameter and two lists of genes, the average profiles don't look right at all. Both gene groups are simply graphed as perfectly vertical lines. This is definitely not correct, they should have a broad looking profile.

Here's my command line:

ceas --name CEAS_TSGTDG --gn-groups=TSG_list.txt,TDG_list.txt --gn-group-names='TSG,TDG' -g ../../../hg19.refGene -b MACSpeaks.bed -w MACS2_treat_pileup.wig

I know that my bed and wig files are good, because I get good output without supplying --gn-groups. I'm wondering if I'm not using the proper format for my "TSG_list.txt" and "TDG_list.txt"? They're simply a list of gene names followed by newlines. Here's an excerpt of TDG_list.txt:

BZRAP1
PEX13
NEK4
RNASEH2B
C12orf57

Am I doing something wrong?

[hartmaier]

I'm trying to run CEAS on two different sets of genes that are present in my ChIP-seq, but it seems as though I'm doing something incorrectly. When I run CEAS without the --gn-groups parameter, I get great results. I see reasonable looking profiles in the wiggle section of the .pdf output.

However, when I run CEAS with the --gn-groups parameter and two lists of genes, the average profiles don't look right at all. Both gene groups are simply graphed as perfectly vertical lines. This is definitely not correct, they should have a broad looking profile.

Here's my command line:

ceas --name CEAS_TSGTDG --gn-groups=TSG_list.txt,TDG_list.txt --gn-group-names='TSG,TDG' -g ../../../hg19.refGene -b MACSpeaks.bed -w MACS2_treat_pileup.wig

I know that my bed and wig files are good, because I get good output without supplying --gn-groups. I'm wondering if I'm not using the proper format for my "TSG_list.txt" and "TDG_list.txt"? They're simply a list of gene names followed by newlines. Here's an excerpt of TDG_list.txt:

BZRAP1
PEX13
NEK4
RNASEH2B
C12orf57

Am I doing something wrong?

I am having the same issue. Did you ever figure this out?

[cjsifuen]

I am having the same issue. Did you ever figure this out?

Same issue here. I guess no one has figured this out yet. :/

[ygc_hku]

You may found my package interesting. https://github.com/GuangchuangYu/ChIPseeker

[cjsifuen]

I am having the same issue. Did you ever figure this out?

I found out what was going on in my case. Essentially, the gene identifiers in the group file were not the same type as in the refgene file. I was using the refgene files from UCSC, which uses refseq mrna nomenclature, but my group text files had ensembl_gene_ids.

I converted the gene names in the group files to refseq mrna ids and the problem was solved.