Dear Sammeth,
I run flux-capacitor in the following options: flux-capacitor -i bamfile -a annotation_file -o ouptut --threads nthreads.
When I run it with an gff annotation file that have some transcripts that overlap each other, but not exons, such as I show in the following example with 3 transcripts or in the attached image dmel.overlap.jpg.
2L selenoprofiles_exonerate exon 4939284 4939788 . + . transcript_id "FBtr0304686.74.homologue"; gene_id "FBgn0304686.74.homologue";2L selenoprofiles_exonerate exon 4891851 4892080 . + . transcript_id "FBtr0304686.74.homologue"; gene_id "FBgn0304686.74.homologue";2L selenoprofiles_genewise exon 4893955 4893994 . + . transcript_id "FBtr0077391.1.homologue"; gene_id "FBgn0077391.1.homologue";2L selenoprofiles_genewise exon 4901402 4901917 . + . transcript_id "FBtr0077391.1.homologue"; gene_id "FBgn0077391.1.homologue";2L selenoprofiles_genewise exon 4902025 4902395 . + . transcript_id "FBtr0077391.1.homologue"; gene_id "FBgn0077391.1.homologue";2L selenoprofiles_genewise exon 4902461 4902593 . + . transcript_id "FBtr0077391.1.homologue"; gene_id "FBgn0077391.1.homologue";2L selenoprofiles_genewise exon 4902664 4902905 . + . transcript_id "FBtr0077391.1.homologue"; gene_id "FBgn0077391.1.homologue";2L selenoprofiles_genewise exon 4902974 4903150 . + . transcript_id "FBtr0077391.1.homologue"; gene_id "FBgn0077391.1.homologue";2L selenoprofiles_genewise exon 4937441 4937468 . + . transcript_id "FBtr0077393.27.homologue"; gene_id "FBgn0077393.27.homologue";2L selenoprofiles_genewise exon 4937534 4938182 . + . transcript_id "FBtr0077393.27.homologue"; gene_id "FBgn0077393.27.homologue";2L selenoprofiles_genewise exon 4938324 4938866 . + . transcript_id "FBtr0077393.27.homologue"; gene_id "FBgn0077393.27.homologue";2L selenoprofiles_genewise exon 4940964 4941363 . + . transcript_id "FBtr0077393.27.homologue"; gene_id "FBgn0077393.27.homologue";
The ouptut results obtained for this example are the following:
2L selenoprofiles_genewise transcript 4893955 4903153 . + . transcript_id "FBtr0077391.1.homologue"; locus_id "2L:4891851-4941366W"; gene_id "FBgn0077391.1.homologue"; reads NaN; length 1482; RPKM NaN
2L selenoprofiles_genewise transcript 4937441 4941366 . + . transcript_id "FBtr0077393.27.homologue"; locus_id "2L:4891851-4941366W"; gene_id "FBgn0077393.27.homologue"; reads NaN; length 1623; RPKM NaN
2L selenoprofiles_exonerate transcript 4891851 4939788 . + . transcript_id "FBtr0304686.74.homologue"; locus_id "2L:4891851-4941366W"; gene_id "FBgn0304686.74.homologue"; reads NaN; length 735; RPKM NaN
As it can be seen the reads and RPKM values are inconsistent. Some parts of the ouput of the execution are shown here. It can be seen that are some errors and warnings that are resposible for these NAN values.
PROFILE] Scanning the input and getting the attributes.
profiling OK (00:23:52)
first round finished .. took 1432 sec.
12325 single transcript loci
377309560 mappings in file
43276718 mappings fall in single transcript loci
4615251872 mappings in annotation-mapped pairs
81,121 min/max read length
[SOLVE] Deconvolving reads of overlapping transcripts.
decomposing [WARN] Fraction inconsistency FBtr0077393.27.homologue -2.304722170272954
...
[ERROR] Failed to set lp output to:
null
java.lang.NullPointerException
at java.io.FileOutputStream.<init>(FileOutputStream.java:206)
at java.io.FileOutputStream.<init>(FileOutputStream.java:136)
at barna.flux.capacitor.reconstruction.GraphLPsolver.run(GraphLPsolver.java:950)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.call(FluxCapacitor.java:1097)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2631)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1886)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:198)
unusual normalization factor: 0.03384014257154664
[WARN] Unsolved system: 2L:4891851-4941363W
[WARN] Fraction inconsistency FBtr0302984.1.homologue -2.313103458721854
Model name: FBtr0080341.1.homologue
Is there a solution for this overlapping case?
Thank you.
Cheers,
Miqueldmel.overlap.jpg