I am a computer scientist just starting out in bioinformatics topics, and would appreciate any guidance that can be given here:
I have an mRNA sequence- an isoform - whose length is about 4000 base pairs (bp) - the origin is provided in the link.
I also have a bam file/fasta file of the entire transcriptome of a kidney cell (see Data Access tab).
My objective is to quantify mRNA expression levels of the mRNA sequence in the transcriptome.
How does one get started? Should I use the original format (TenX bam, about 10 GB) or SRA archive data (fasta, about 3.5 GB)? Why are the files so different in size?
I have a MacBook with
samtools installed and 16GB of RAM. Is this enough to process the data and what basic commands should be used to quantify the 4000 bp sequence overlaps in the transcriptome?