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5.2 years ago
ustcxijing
•
0
My background is plant biology. I know little about programming and bioinformatics. I have ~60 plant lncRNAs from RNA seq, and need to figure out their possible mRNA targets in the whole plant transcriptome. I have tried LncTar and would like to use RIblast to confirm the analysis results of LncTar. Does someone use RIblast? The only information about RIblast that I can find is on https://github.com/fukunagatsu/RIblast. I could not find somewhere to download this software and don't know where to write the scripts that provided on the above-mentioned webpage. Please give me suggestions if someone used this software before. Thanks a lot!
Don't know the tool, but:
To get the scripts use the clone command (google git for more info):
git clone https://github.com/fukunagatsu/RIblastTo install the software you use make, type this command while you are in the cloned folder:
makeSlightly more info: https://stackoverflow.com/questions/7751342/how-to-execute-make-file
Thanks, gb! I will try what you suggested.
I cloned the all RIblast folders on my computer, but I can't install the software by running "make". It says"command not found". Should I install "make"?
Yes, think you can do it with this command:
sudo apt-get install build-essentialThanks, gb. The command works! I have successfully cloned and installed the software in my computer.
I'm trying to run the job with the scripts listed on GitHub. According to the instruction, I need to convert my FASTA database file (a whole transcriptome) to db file with "db" command. When I tried to convert it the first time, I got the response back very quickly. And it seemed that I got three correct files with db.nam, db.bas and db.acc extension. However, when I tried to run the analysis with "ris" command, it returned that "can't open my database file_db.seq".
I thought it might be due to long file name. So I shortened my database file name and tried to converted it again with "db" command. When I wrote the command, the windows PowerShell suggested me adding ".\" before my FASTA formatted file name. I followed the suggestion. However, it's taking long time to convert. I started yesterday late afternoon, and it has not finished converting this morning yet. I got the two files with db.nam, db.bas very quickly. Their size is the same compared with that I previously obtained. But, the file with db.acc is not ready yet. I can see the file size is increasing (It is already 203,317kb). My original transcriptome file in FASTA format is only 95,011kb!
Do you know what is the possible reason? Any suggestions about that? Thanks a lot!