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Old 11-04-2009, 10:43 AM   #1
Junior Member
Location: Montreal

Join Date: Oct 2009
Posts: 1
Default to aligning all reads with SHRiMP (as automatic)


I'm new in SHRiMP. I have 10 library and for each library, i had used the of SHRiMP to 1000 files. Then, i have 1000 files csfasta type for on library. I had test some of them with rmapper-cs... to align and it's working but i need to run the same command as automatically for the 1000 files csfasta first and for all 10 library.
The command line is like:
./rmapper-cs -m 8 -i -30 -g -35 -e -7 -x -25 -h 70% -v 65% -M 35bp,fast -o 100 -U /root/Desktop/SHRiMP_1_3_0/readsT/1000_to_1999.csfasta /root/Desktop/DB.fasta > /root/Desktop/SHRiMP_1_3_0/results/res_1000_to_1999.out

I try with command find like this one:


find /root/Desktop/SHRiMP_1_3_0/readsT/ -name "*.csfasta*" -exec /root/Desktop/SHRiMP_1_3_0/bin/rmapper-cs -m 8 -i -30 -g -35 -e -7 -x -25 -h 70% -v 65% -M 35bp,fast -o 100 -U "{}" /root/Desktop/docShrimp191009/DB.fasta >> /root/Desktop/SHRiMP_1_3_0/results/"{}"res_U_lib1.out {} \;

but it said bad file and nothing in result file

Do you know what's the problem

ps: {} is just to have the name of the file in result, it does't working but for the input file it's ok

ahabnar is offline   Reply With Quote

align, automatic, color code cs, reads, shrimp

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