I am interested in the software of MuSiC and now trying to inplement it. When I use the calc-wig-covg function with the command of
Genome music bmr calc-wig-covg –wig-list=/home/share/input/wig_list.txt –output-dir=/home/share/output –reference-sequence=/home/share/input/allgenome_hg18.fa –roi-file=/home/share/input/roi.tsv
I got the following errors
Use of uninitialized value of $tot_covd in concatenation (.) or string at /usr/.../CalcWigCovg.pm line 229
And in all the output files, the covg of all samples in all genes are 0. I am not sure whether this error is due to my input file, so I attached some lines of each input file below:
TCGA-02-0003-01 /home/share/input/stddata_2012_08_25/GBM/Coverage/TCGA-02-0003-01.wig TCGA-02-0033-01 /home/share/input/stddata_2012_08_25/GBM/Coverage/TCGA-02-0033-01.wig ...
reference file was downloaded from UCSC by
and "cat" them all together:
>chr10 ****** >chr11 **** ...
chr1 87100715 87152695 SEPT15 chr2 109657664 109729072 SEPT10 chr2 241903395 241942114 SEPT2 chr4 78089918 78178792 SEPT11 chr4 164668498 164754226 MARCH1 chr5 10406827 10488491 MARCH6 chr5 126233449 126394145 MARCH3 ...
Also, I found that ROI files must be in ordered, otherwise there are errors. But I am not quite sure based on which order, chromosome or start pos? For example, if I put "chr1 5 10 gene1" before "chr1 1 3 gene1", an error will show up said that the first start pos is bigger than the second one. So I am thinking if the two start pos are 10 and 5, which order should put them, based on the number value or number itself? And also, does all these orders obey chr 1-22, i.e., chr1 is all alway before chr2?
Can somebody explain the above problems? Thanks in advance.