simoncchu / splicejumper Goto Github PK
View Code? Open in Web Editor NEWA tool for splicing junction calling from RNA-Seq data
splicejumper's Introduction
Usage: ./SpliceJumper [options]
Required options:
-P/G indicates collecting features / indicates output results
-r FILE reference file(indexed)
-b/i FILE input bam/prediction file(index and sorted)
-o FILE output file name
-l INT read length
Optimal options
-c INT slack value for split position with default 3
-m DOUBLE mean insert size
-v DOUBLE standard variation of insert size
1.Feature collection:
./SpliceJumper -P -r ./human_g1k_v37.fasta -b ./simulated_data_input.bam -o test_sim.txt -l 100 -c 5
2. Training and prediction
2.1 Training
python easy.py training_data
2.2 Predicting
..\windows\svm-predict data.scale Trained.model predictResult
3. Output generated splicing junctions
./SpliceJumper -G -i prediction.txt -o result.txtsplicejumper's People
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xtmgahsplicejumper's Issues
compilation failed
--hello,
compilation failed with:
g++ -O3 -Wall -I../bamtools/include -L../bamtools/lib -Wl,-rpath,../bamtools/lib -o JunctionClassifier_1 public_func.o Alignment.o bam_parse.o Coverage.o fai_parser.o fasta_parser.o ReferenceSeq.o local_alignment.o CandidateSitesCaller.o TrainingSet.o HardClipReads.o main.o
-lbamtools -lz -lm
local_alignment.o: In function LocalAlignment::align(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&)': local_alignment.cpp:(.text+0x6be0): undefined reference to std::__throw_out_of_range_fmt(char const*, ...)'
CandidateSitesCaller.o: In function CandidateSitesCaller::alignSoftClip(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int*&, int*&)': CandidateSitesCaller.cpp:(.text+0x7354): undefined reference to std::__throw_out_of_range_fmt(char const*, ...)'
CandidateSitesCaller.cpp:(.text+0x753c): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
collect2: ld returned 1 exit status
make: *** [SpliceJumper] Error 1
install problem
Here is what I got:
make all
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c bam_parse.cpp
clang: warning: -Wl,-rpath,../bamtools-master/lib: 'linker' input unused
clang: warning: argument unused during compilation: '-L../bamtools-master/lib'
In file included from bam_parse.cpp:1:
./bam_parse.h:4:10: fatal error: 'api/BamReader.h' file not found
include "api/BamReader.h"
^
1 error generated.
make: *** [bam_parse.o] Error 1
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