Hello I try to analyse my CLIP-seq data and a corresponding control inform of a normal RNA-seq data set. I think Piranha should be designed to do exactly this. Unfortunately I can not manage to install piranha with the bam file read support. Therefore I have three question, with the hope that some of you can help me out there:
1/ does anyone know a better way to analyse this kind of data? 2/ if I can not use Piranha with bam read support (-bin_size and -bin_size_covars options), I can still provide binned read count data. What is the appropriate way to provide the covariates in this scenario? 3/ Can someone give me a hint how I can make Piranha install using the bam file read options via bamtools? I have installed bamtools 2.5.1. If I call the piranha 1.2.1 configure via:
./configure --with-bam_tools_headers="${HOME}/.local/include/bamtools/" --with-bam_tools_library="${HOME}/.local/lib64/"
I get:
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
provided BAMTools headers directory is ${HOME}/.local/include/bamtools/
provided BAMTools library directory is ${HOME}/.local/lib64/
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether we're compiling on Darwin/MacOS... no
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for linking against gsl matrix... yes
checking for BAMTools... no
configure: WARNING: could not find BAMTools, disabling BAM support
configure: creating ./config.status
config.status: creating Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
config.status: creating src/test/regressionTests.xml
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
bamtools 2.5.1 is installed and the content of the lib and include directories are:
tree ${HOME}/.local/include/bamtools/
${HOME}/.local/include/bamtools/
├── api
│ ├── algorithms
│ │ └── Sort.h
│ ├── api_global.h
│ ├── BamAlgorithms.h
│ ├── BamAlignment.h
│ ├── BamAux.h
│ ├── BamConstants.h
│ ├── BamIndex.h
│ ├── BamMultiReader.h
│ ├── BamReader.h
│ ├── BamWriter.h
│ ├── IBamIODevice.h
│ ├── SamConstants.h
│ ├── SamHeader.h
│ ├── SamProgramChain.h
│ ├── SamProgram.h
│ ├── SamReadGroupDictionary.h
│ ├── SamReadGroup.h
│ ├── SamSequenceDictionary.h
│ └── SamSequence.h
└── shared
└── bamtools_global.h
tree ${HOME}/.local/lib64/
${HOME}/.local/lib64/
├── libbamtools.a
└── pkgconfig
└── bamtools-1.pc
I tried several other strategies and used hints I found online, without any improvment. Therefore I decided to contact you directly. Any help highly appreciated.
Thank you very in advance.
