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 usingsamtools 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 achr
prefix has been added to the fields with chromosome names.- [EXTEND THIS LIST WHEN ADDING MORE TEST FILES TO THE DIRECTORY]