Requires short-read FASTQ file(s) to assemble and HISAT2 and GMAP indexes of the same reference genome Example: ./create_sr_rna.py -1 pair1.fq -2 pair2.fq -H hisat2_ref -G gmap_ref -o out_dir/ Final super-read + short read alignments can be found in out_dir/sr_merge.bam ...
In order to build StringTie from this GitHub repository the following steps can be taken: git clone https://github.com/mpertea/stringtie2 cd stringtie2 make release Note that simply running make will produce an executable which is more suitable for debugging and runtime checking but which can...
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git clone https://github.com/gpertea/stringtie cd stringtie make -j4 release During the first run of the above make command a few library dependencies will be downloaded and compiled, but any subsequent stringtie updates (using git pull) should rebuild much faster. To complete the installation...
EgeDede562mentioned this issueSep 18, 2018 laurentierneymentioned this issueOct 30, 2020 Open Sign up for freeto join this conversation on GitHub. Already have an account?Sign in to comment
Hi, thanks for the wonderful tool for long RNA reads analysis~ I am trying to run StringTie2 for rice ONT raw reads (fastq reads) by first running the uLTRA aligner (v0.0.4) and then provide generated sorted bam file to StringTie (v2.2.1...
master stringtie/gclib/ Go to file Latest commitgpertea minor GSam cleanup b56f9e5 on Jul 18 Git stats History FilesType Name Latest commit message Commit time . . GArgs.cpp fix gargs 3 years ago GArgs.h more MacOS gdb fixes 4 years ago GBase.cpp minor gclib optimizations 15 ...
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git clone https://github.com/gpertea/stringtie cd stringtie make -j4 release During the first run of the above make command a few library dependencies will be downloaded and compiled, but any subsequent stringtie updates (using git pull) should rebuild much faster. To complete the installation...