First of all, many thanks for developing this amazing tool.
I have been used without problems for single-end reads, however, I 'm receiving the following error when I try to use for .bam files originated from .bedpe files.
The error:
$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper$ ngs.plot.r -G hg19 -R genebody -C config_ngsplot.txt -O metaplot_HiCHIPxHiCxChIPseq -L 5000
Configuring variables...
Using database:
~/Desktop/Software/ngsplot-develop/database/hg19/hg19.ensembl.genebody.protein_coding.RData
Done
Loading R libraries.....Done
Analyze bam files and calculate coverageopen: No such file or directory
Error in FUN(X[[i]], ...) : failed to open SAM/BAM file
file: '~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper/Hi-C-Input_sorteds_interaction.bam'
Calls: headerIndexBam ... indexBam -> sapply -> sapply -> lapply -> FUN -> .Call
Execution halted
$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper
Hi Raphael,
Did you figure out the issue and solution for that? i am also facing same issue. please let me know if you have any suggestion.
best,
sachin
First of all, many thanks for developing this amazing tool.
I have been used without problems for single-end reads, however, I 'm receiving the following error when I try to use for .bam files originated from .bedpe files.
The error:
this is the file
I saw this closed thread https://github.com/shenlab-sinai/ngsplot/issues/9, but not sure if it applies to my case.
Is there a way to use this type of file as input?
Many thanks,
Raphael