RNA-Seq BAM File Quality Control with RSeQC (Drosophila melanogaster)
This example dataset contains RNA-Seq reads that have been mapped (STAR) to their genome (Drosophila melanogaster). Some obtained BAM files together with the latest structural annotation (GFF) are provided here to show an exemplary usage of “BAM Quality Control” in OmicsBox.
Information about the experiment.
Single and Paired-End
Link to the public repositories where the original data can be found:
Convenient website to download the files from NCBI https://sra-explorer.info/#
1- Analysis Step
Input BAM files
2 samples have been selected and further reduced in size (samtools view -bo subset.bam -s 123.1 alignments.bam chr1 chr2).
Annotation file (Gene Model)
GFF has to be extracted before providing it.
Provide the Annotations mentioned above
Extract the GFF before providing it
2:20 for the 2 subsetted samples and annotations provided