By mistake the SFF file was deleted once the Amplicon Full processing pipeline was done. How can we reprocess the data to generate the SFF file back again?
Thanks!
Thanks!
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Sadly the gsReporter application will not produce SFF files from an exiting analysis directory; SFF files can only be generated by gsRunProcessor. But you don't have to repeat the entire Signal Processing pipeline, you can perform an Analysis Filter job on the existing D_ directory which will take far less time.Originally posted by Xterra View Post
If you are unfamiliar with how to perform a Filter only analysis (these steps assume your current working directory to be the run (R_) directory and the Full Amplicon analysis directory (D_) still exists there):
1. Create a template file with the default amplicon filter settings, saving it to a file named (e.g.) ampliconFilter.xml:
2. Run the filter only analysis pipeline providing the name of the template file you just generated and the existing analysis (D_) direcotry.Code:# gsRunProcessor --template=filterOnlyAmplicon > ampliconFilter.xml
The filter only pipeline runs much faster than the full analysis pipeline. You will have a new, complete D_ directory with the SFF files.Code:# runAnalysisFilter --pipe=./ampliconFilter.xml <D_directory_name>
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kmcarr
I actually did exactly what you suggested but the new D directory did not included the SFF file on the regions subfolder.Comment
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The SFF files are not in the regions subfolder. There should be a separate subdirectory named 'sff'.Originally posted by Xterra View PostComment
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kmcarr
Sorry that's what I meant. Now, I am not quite sure what's going on, I repeated the process three time and I finally got the SFF file. However, when I split the MID, I can see I got very few reads/MID. When I split the original SFF file that came out of the run, I had plenty of reads per MID. Therefore, something is wrong.
Now, I can see the fasta and qual files, can I split the MID from the fasta file using any of the SFF tools?Last edited by Xterra; 10-31-2011, 08:19 AM.Comment
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Why do want to do that? You should investigate on what is going wrong with your filtering job ...Originally posted by Xterra View Post
just my 2p,
SvenComment
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At this point I am more interested on retrieving my data.
Do you know of any tool I can use to split the MID using the central FASTA file that was generated during the run?Comment
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You finally will need to find out what was wrong, believe me ... :-)
Nevertheless, one of the tools capable of doing what you want might be "FASTX Barcode Splitter" from the fastx toolkit (http://hannonlab.cshl.edu/fastx_tool...splitter_usage).
hth, SvenComment
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sklages
Thanks! I will check it out.Comment
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