Tweet
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!
-
-
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>
-
kmcarr
I actually did exactly what you suggested but the new D directory did not included the SFF file on the regions subfolder.Comment
-
The SFF files are not in the regions subfolder. There should be a separate subdirectory named 'sff'.Originally posted by Xterra View PostComment
-
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
-
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
-
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
-
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
-
sklages
Thanks! I will check it out.Comment
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment