I've emailed the samifier developers.Ĭ16582 GLEAN gene 35 385.
#Geneious tutorial for lastz code#
He looked around in the java code and figured out that the problem actually seems to be with the mzid file. Giles and I made another version of the gff file, but still got the same error. Still got the same error.Ĭ16582 GLEAN gene 35 385. The above file did not actually look like the example the samifier developers had given me, so re-edited the file and reran code. I think the error was "Run exception thrown", but I'm not sure what this meansĪbbreviated gff file so that it only has a few entries and made sure that the "gene" line came before mRNA and exon lines. The code ran, but all I got was an empty log file. Java -jar samifier.jar -r /Volumes/web/oyster/proteomics/interact-20120821_103B_251_QE_02.prot.mzid -m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Volumes/web/cnidarian/ets_v9_r.gff -c /Volumes/web/oyster/bioinformatics/Crassostrea_gigas.GCA_000297895.1.21.fa -o /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/Cg_samifier_out20141313 -l /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/log_20141313 -b /Users/emmatimminsschiffman/Documents/winter_2014/Cg_20141313.bed I added this to one of the files that Steven had made (ets_v9_r.gff) and ran the following in samifier Giles found a webpage ( ) that says that the #gff-version3 must be in the header of a gff3 file. Java -jar samifier.jar -r /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/F003797.mzid -m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Users/emmatimminsschiffman/documents/winter_2014/Bioinformatics/ets_v9_r.giles.gff -c /Volumes/web/cnidarian/v9_multi -o /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/Cg_samifier_out2014319 -l /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/log_2014319 -b /Users/emmatimminsschiffman/Documents/winter_2014/Cg_2014319.bed I exported the search results to use in samifier and the file export parameters can be found here. Jimmy ran a mascot search on one of my files and it took 2 days to run. Java -jar samifier.jar -r /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/F003797.mzid -m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Volumes/web/cnidarian/ets_v9_g.gff -c /Volumes/web/cnidarian/v9_multi -o /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/Cg_samifier_out2014320 -l /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/log_2014320 -b /Users/emmatimminsschiffman/Documents/winter_2014/Cg_2014320.bed Running through all of the gff files that Steven made to see if any work. mRNA and cds need ID=mRNAXXXXX or ID=cdsXXXXX gene line needs to be first entry for each scaffoldģ. List of things that need to be changed in bottom gff file (v9_p.gff):ġ. The bottom file is an example of a gff file that needs to be edited to mimic the top. The top file in this picture (in pink box) is the short file that seems to work.
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