Hello!

Can i use funseq2 for scoring CODING variants? In papers funseq2 is used for scoring non-coding drivers.

Based on the instructions I read, running make can solve the problem of TFMpvalue installation for FunSeq2 but when I do so I get this error:
[root@node10 TFM-Pvalue]# make
g++ -O3 -DJASPAR=1 -DPROGRAM=0 TFMpvalue.cpp Matrix.cpp ArgumentException.cpp FileException.cpp ParseException.cpp -o TFMpvalue-pv2sc
TFMpvalue.cpp: In function ‘void arguments(int, char* const*)’:
TFMpvalue.cpp:503:45: error: ‘getopt’ was not declared in this scope
while (((option = getopt(argc,argv,options)) != EOF)) {
^
TFMpvalue.cpp:507:23: error: ‘optind’ was not declared in this scope
OPTIONS[option] = optind-1;
^
make: *** [TFMpvalue-pv2sc] Error 1

Hi,

I am trying to run funseq2. I installed TFMpvalue. I can run ./TFMpvalue-sc2pv from funseq2 directory.
But when I run the command,It's asking me to run it again.

./funseq2.sh -f HT_variants_sorted.bed -inf BED -nc
Please install TFMpvalue-sc2pv!

Can you please tell me what is going on here?

Thank you,
Parvathi.

Hey,

do you plan to provide prebuilt data context for the hg38 assembly anytime soon or will the tool stick with hg19?