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Old 07-19-2011, 01:05 PM   #1
clostridium40
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Default sff_extract problems

You will have to forgive me but I know very little about Linux and python, I have installed MIRA in order to assemble 454 reads and Illumina reads from a couple of bacterial genomes. However, before I can run MIRA with 454 reads I need to remove the adaptor sequence, so they suggest using sff_extract. I went to the website http://bioinf.comav.upv.es/sff_extract/index.html, but when I click on the download link it just gives me the line code for the program. I do not know what to do with this code in order to get the program loaded, so that I can trim my sequences for MIRA. I also do not have access to the sfftools that come with the 454/Roche software package as the sequencing was outsourced to a company and they claim not to know what I'm talking about when I ask for them. Any help would be very much appreciated, I appreciated everyone's help answering my stupid questions. Thank you in advance.
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Old 07-20-2011, 12:57 PM   #2
clostridium40
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Ignore this post, another newbie who had hit a wall, but I figured out the answer.
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Old 07-21-2011, 05:08 AM   #3
Eric Fournier
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For anyone who would stumble on this post and wonder what the solution is:

sff_extract is a python script. It needs to be run with the python interpreter.
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