Dear users,
I have recently started analyzing RNA-Seq data for gene expression analysis, hence am quite new to the field.
I have used STAR for aligning RNA-Seq reads (hg38, Ensemble, release 94) using --quantMode TranscriptomeBAM for STAR run.
When I analyzed the quality of BAM files (2 files - genomic BAM and Aligned.toTranscriptome.bam) using BamQC, I get widely different results in terms of basic statistics like primary alignments
In whole in genomic BAM, total 96.95 reads fall in primary alignment, transcriptome BAM has only 29.4% primary aligned reads. Does this low % means the data quality is bad for doing analysis like differential isoform and allele expression?
Thanks for your inputs.
I have recently started analyzing RNA-Seq data for gene expression analysis, hence am quite new to the field.
I have used STAR for aligning RNA-Seq reads (hg38, Ensemble, release 94) using --quantMode TranscriptomeBAM for STAR run.
When I analyzed the quality of BAM files (2 files - genomic BAM and Aligned.toTranscriptome.bam) using BamQC, I get widely different results in terms of basic statistics like primary alignments
In whole in genomic BAM, total 96.95 reads fall in primary alignment, transcriptome BAM has only 29.4% primary aligned reads. Does this low % means the data quality is bad for doing analysis like differential isoform and allele expression?
Thanks for your inputs.
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