miRExpress

[hsmart]

Hi All,

We like to use miRExpress software (http://mirexpress.mbc.nctu.edu.tw/) for our microRNA-seq data. I tried to run the example file however I am getting error as Segmentation fault with /miRExpress/bin/analysis script. Can you please help me with it? Also, it does not generate any particular output with alignmentSIMD script apart from no-hit file and a temp directory.
I am running following commands:
/miRExpress/bin/Raw_data_parse -i /Example/example
/miRExpress/bin/Trim_adapter -i /Example/example.merge -t /Example/3_adaptor.txt
/miRExpress/bin/statistics_reads -i /Example/example.merge.trim
/miRExpress/bin/alignmentSIMD -r data/hsa_precursor.txt -i /Example/example.merge.trim -o /Example/Output/ -t 0.9 -n /Example/Output/Example_nohit.txt
/data/hemang/Software/Sequencing/miRNA/miRExpress/bin/analysis -r data/hsa_precursor.txt -m data/hsa_miRNA.txt -d /Example/Output -o /Example/Example_alignment.txt -t /Example/example_expression.txt

Thanks for your kind help,

Best wishes,

Rakesh

[bfantinatti]

Hello hsmart, I think you have a compilation problem. Did you compile this program, or just used the executables that came inside the src folder? If you are using these files, I suggest to compile your own files. (./configure > make #make install).
For your convenience, after compiling your own executables, you cam move them to the PATH$. I use /usr/local/bin. Just copy the executables there (alignmentSIMD, analysis, Raw_data_parse, statistics_reads and Trim_adapter) and you can execute them from anywere. Is easier to let your adapter sequence, files do process and precursor and miRNA database in the same folder. Try this and let me know.
Best wishes