latest version v1.9f bugs with Gencode annotation

[JamalEH]

Dear Woody, May this find you healthy and safe!

I just realized that the latest version of PSIsigma is reporting a bug when run with Genocode.annotation.v27.gtf file. All the steps actually run correctly but the bug occurs at the filtering step of the splicing events based on the selected mode 0 1 2 3. I included below the bug that occurred. this is happening whatever the pre-filtering mode I've used. The gtf file is the same one I used when ran STAR. This did not happen with previous versions.

Thank you so much for your help!

Best regards, Jamal.

gtf = gencode.v27.annotation.sorted.gtf name = PSIsigma type = 1 nread = 5 skipratio = 0.05 fmode = 0 irmode = 1 Path = /vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/siRNA/alignment/PSI-Sigma-1.9f Sample_siRNA_CTRL_A.Aligned.sortedByCoord.out.bam.bai is ready. Sample_siRNA_CTRL_B.Aligned.sortedByCoord.out.bam.bai is ready. Sample_siRNA_CTRL_C.Aligned.sortedByCoord.out.bam.bai is ready. Sample_siRNA_ERa_A.Aligned.sortedByCoord.out.bam.bai is ready. Sample_siRNA_ERa_B.Aligned.sortedByCoord.out.bam.bai is ready. Sample_siRNA_ERa_C.Aligned.sortedByCoord.out.bam.bai is ready. Generating mapping file... Checking splice-junction files... ===Splice-junction files spent 0.0000 hours.=== ===Database spent 0.0000 hours.=== Getting intron reads.... Checking Sample_siRNA_CTRL_C.Aligned.sortedByCoord.out.bam... Checking Sample_siRNA_CTRL_C.IR.out.tab... Sample_siRNA_CTRL_C.IR.out.tab existed. Pass... Checking Sample_siRNA_CTRL_A.Aligned.sortedByCoord.out.bam... Checking Sample_siRNA_CTRL_A.IR.out.tab... Sample_siRNA_CTRL_A.IR.out.tab existed. Pass... Checking Sample_siRNA_CTRL_B.Aligned.sortedByCoord.out.bam... Checking Sample_siRNA_CTRL_B.IR.out.tab... Sample_siRNA_CTRL_B.IR.out.tab existed. Pass... Checking Sample_siRNA_ERa_C.Aligned.sortedByCoord.out.bam... Checking Sample_siRNA_ERa_C.IR.out.tab... Sample_siRNA_ERa_C.IR.out.tab existed. Pass... Checking Sample_siRNA_ERa_A.Aligned.sortedByCoord.out.bam... Checking Sample_siRNA_ERa_A.IR.out.tab... Sample_siRNA_ERa_A.IR.out.tab existed. Pass... Checking Sample_siRNA_ERa_B.Aligned.sortedByCoord.out.bam... Checking Sample_siRNA_ERa_B.IR.out.tab... Sample_siRNA_ERa_B.IR.out.tab existed. Pass... ===Intron-read file spent 0.0000 hours.=== Ready to do PSI analysis... Group A has 3 samples. Group B has 3 samples. Reading... Sample_siRNA_CTRL_A Reading... Sample_siRNA_CTRL_A.SJ.out.tab accession = Sample_siRNA_CTRL_A (N) Sample_siRNA_CTRL_A Checking IR reads checking... Sample_siRNA_CTRL_A.IR.out.tab Checking SJ reads... Reading... Sample_siRNA_CTRL_B Reading... Sample_siRNA_CTRL_B.SJ.out.tab accession = Sample_siRNA_CTRL_B (N) Sample_siRNA_CTRL_B Checking IR reads checking... Sample_siRNA_CTRL_B.IR.out.tab Checking SJ reads... Reading... Sample_siRNA_CTRL_C Reading... Sample_siRNA_CTRL_C.SJ.out.tab accession = Sample_siRNA_CTRL_C (N) Sample_siRNA_CTRL_C Checking IR reads checking... Sample_siRNA_CTRL_C.IR.out.tab Checking SJ reads... Reading... Sample_siRNA_ERa_A Reading... Sample_siRNA_ERa_A.SJ.out.tab accession = Sample_siRNA_ERa_A (T) Sample_siRNA_ERa_A Checking IR reads checking... Sample_siRNA_ERa_A.IR.out.tab Checking SJ reads... Reading... Sample_siRNA_ERa_B Reading... Sample_siRNA_ERa_B.SJ.out.tab accession = Sample_siRNA_ERa_B (T) Sample_siRNA_ERa_B Checking IR reads checking... Sample_siRNA_ERa_B.IR.out.tab Checking SJ reads... Reading... Sample_siRNA_ERa_C Reading... Sample_siRNA_ERa_C.SJ.out.tab accession = Sample_siRNA_ERa_C (T) Sample_siRNA_ERa_C Checking IR reads checking... Sample_siRNA_ERa_C.IR.out.tab Checking SJ reads... Number of events = 284764 Number of samples = 6 Statistics option = Two sample t-test number of p-value = 216747 Number of final p-value = 213543 Doing adjust p-values... number of fdr(BH) = 213543 ===PSI analysis spent 1.9644 hours.=== Filtering ΔPSI results... Filtering mode = 0 Reading... gencode.v27.annotation.sorted.gtf.mapping.txt Reading... PSIsigma.db (ERROR) 18790, STX18 can't find wings in the database. Aborting... ===Filtering spent 0.0025 hours.===

***Total: 1.9669 hours (or 118.014mins).

[wososa]

@JamalEH ,

Thanks for reporting the bug. Sorry for the late reply. I just tried to download .gtf from https://www.gencodegenes.org/. PSI-Sigma v1.9h works fine. Please download v1.9h (https://github.com/wososa/PSI-Sigma/releases/tag/v1.9h) and delete the PSIsigma.db file before you re-run.

Thanks, Woody

[JamalEH]

Dear Woody, Thank you for your feedback!

I hereby confirm that the latest version "v1.9h" runs correctly with Gencode annotation.

Best regards, Jamal.