test_data

Test data for APAeval

Use the files provided here for developing, debugging, testing your code.

• .bam files with index files (.bam.bai) as inputs for execution workflows ([Created by choosing 2 genes with MACE-seq PAS reads at at least 2 sites (GSE151724) and subsetting bam files (generated for the pilot_benchmark: siControl_R1, SRR11918577 and siSrsf3_R1, SRR11918579) to reads contain reads falling within +/- 1kb from gene boundaries from the gtf file]).
• .fastq files can be generated to test alignments using samtools bam2fq input.bam > output.fastq.
• corresponding .gtf ([Created GENCODE release M18 subsetted to the 2 genes for the test data with leading "chr" removed to match bam files])
• corresponding .gff3 ([Created GENCODE release M18 subsetted to the 2 genes for the test data with leading "chr" removed to match bam files])
• .MACEseq.mm10.bed as a ground truth example files ([BED6 files for clevage and poly(A) sites for the 2 genes from the two samples (siControl_R1, SRR11918617 and siSrsf3_R2, SRR11918619) where the score column corresponds to the TPM for each PAS detected by MACE-seq in that sample])
• .bam, .bam.bai, .gtf, .gff3 and .bed files containing _Chr_prefix in the filename. These were generated from their counterparts without the string by adding a chr prefix has been added to the fields with chromosome names.
• [EXTEND THIS LIST WHEN ADDING MORE TEST FILES TO THE DIRECTORY]