churchill-lab / emase-zero Goto Github PK
View Code? Open in Web Editor NEWC++ Implementation of EMASE
Home Page: http://churchill-lab.github.io/emase-zero/
License: MIT License
C++ Implementation of EMASE
Home Page: http://churchill-lab.github.io/emase-zero/
License: MIT License
In the GitHub page http://churchill-lab.github.io/emase-zero/ you mentioned using transcript-lengths file which contained information about the transcripts being maternal or paternal (e.g. ENSMUST00000000001_M (maternal) and ENSMUST00000000001_P (paternal)).
Can you please describe how did you identify the transcripts with maternal and paternal allele?
Did you use any particular method to identify them?
Hi,
I have a client interested interested in single cell ASE based on the 10x Genomics platform. The default Cell Ranger pipeline (using STAR 2.5) is not capable of resolving ambiguously mapped reads across a diploid genome and she is in need of another option. Any suggestions?
Thanks in advance,
Chris
Hi, I am finding difficult to get started with emase-zero. I am following this protocol suggested on the webpage
$ bowtie -q -a --best --strata --sam -v 3 -m 100 bowtie.transcriptome my_sample.fastq | samtools view -bS - > my_sample.bam
$ alntools bam2ec -t transcripts.lengths.tsv -c 8 my_sample.bam my_sample.bin
$ emase-zero -m 2 -b my_sample.bin -o emase-zero.quantified -l transcript.lengths.tsv -g gene2transcripts.tsv
My doubts are:
bowtie.transcriptome
file comes from? is it bowtie index for the reference transcriptome or is it for a personalised transcriptome?bowtie.transcriptome
used in the first step?Do you have working example with some test files that I could follow?
Thanks a lot in advance.
Regards,
Inti
Hi,
I am running into a problem when I try to compile emase-zero. I get the following error:
g++ -lz -o emase-zero alignment_incidence_matrix.o sample_allelic_expression.o alignment_import.o emase.o
alignment_import.o: In function `getBinFormat(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
alignment_import.cpp:(.text+0x404): undefined reference to `gzopen'
alignment_import.cpp:(.text+0x40f): undefined reference to `gzrewind'
alignment_import.cpp:(.text+0x421): undefined reference to `gzread'
alignment_import.cpp:(.text+0x429): undefined reference to `gzclose'
alignment_import.o: In function `readIntFromFile(gzFile_s*, std::basic_ifstream<char, std::char_traits<char> >&)':
alignment_import.cpp:(.text+0x8f7): undefined reference to `gzread'
alignment_import.o: In function `readCharFromFile(gzFile_s*, std::basic_ifstream<char, std::char_traits<char> >&)':
alignment_import.cpp:(.text+0x977): undefined reference to `gzread'
alignment_import.o: In function `fileSeek(gzFile_s*, std::basic_ifstream<char, std::char_traits<char> >&, long)':
alignment_import.cpp:(.text+0x9f2): undefined reference to `gzrewind'
alignment_import.o: In function `loadNFromBin(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, AlignmentIncidenceMatrix&, int)':
alignment_import.cpp:(.text+0xcfe): undefined reference to `gzopen'
alignment_import.cpp:(.text+0x1006): undefined reference to `gzrewind'
alignment_import.cpp:(.text+0x1016): undefined reference to `gzseek'
alignment_import.cpp:(.text+0x103b): undefined reference to `gzread'
alignment_import.cpp:(.text+0x1064): undefined reference to `gzread'
alignment_import.cpp:(.text+0x1087): undefined reference to `gztell'
alignment_import.cpp:(.text+0x10b6): undefined reference to `gzrewind'
alignment_import.cpp:(.text+0x10c6): undefined reference to `gzseek'
alignment_import.cpp:(.text+0x10ee): undefined reference to `gzread'
alignment_import.cpp:(.text+0x111e): undefined reference to `gzread'
alignment_import.cpp:(.text+0x1165): undefined reference to `gzrewind'
alignment_import.cpp:(.text+0x1177): undefined reference to `gzseek'
alignment_import.cpp:(.text+0x1228): undefined reference to `gzread'
alignment_import.cpp:(.text+0x12a5): undefined reference to `gzrewind'
alignment_import.cpp:(.text+0x12b7): undefined reference to `gzseek'
alignment_import.cpp:(.text+0x1350): undefined reference to `gzread'
alignment_import.o: In function `loadFromBin(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
alignment_import.cpp:(.text+0x1a17): undefined reference to `gzopen'
alignment_import.cpp:(.text+0x1c91): undefined reference to `gzread'
alignment_import.cpp:(.text+0x1cb6): undefined reference to `gzread'
alignment_import.cpp:(.text+0x1ddc): undefined reference to `gzread'
alignment_import.cpp:(.text+0x1e3c): undefined reference to `gzread'
alignment_import.cpp:(.text+0x2016): undefined reference to `gzread'
alignment_import.o:alignment_import.cpp:(.text+0x2361): more undefined references to `gzread' follow
alignment_import.o: In function `loadFromBin(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
alignment_import.cpp:(.text+0x51cb): undefined reference to `gztell'
alignment_import.cpp:(.text+0x5260): undefined reference to `gzread'
alignment_import.o: In function `fileSeek(gzFile_s*, std::basic_ifstream<char, std::char_traits<char> >&, long)':
alignment_import.cpp:(.text+0xa1a): undefined reference to `gzseek'
alignment_import.o: In function `fileTell(gzFile_s*, std::basic_ifstream<char, std::char_traits<char> >&)':
alignment_import.cpp:(.text+0xa93): undefined reference to `gztell'
collect2: error: ld returned 1 exit status
Makefile:9: recipe for target 'emase-zero' failed
make: *** [emase-zero] Error 1
It seems to work when I move the zlib linker flag (-lz
) to the end:
g++ -o emase-zero alignment_incidence_matrix.o sample_allelic_expression.o alignment_import.o emase.o -lz
I found this on the topic: https://stackoverflow.com/questions/9417169/why-does-the-library-linker-flag-sometimes-have-to-go-at-the-end-using-gcc
Thank,
Jonas
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