How to calculate gene expression levels

[sekhwal]

Hi, I have output file (sorted BAM) generated from hisat2-2.2.0 pipeline, a reference fasta file and fastq file of MinION. Please let me know the command to RUN RSEM to analysis my data.

[sekhwal]

Hi, I have output file (sorted BAM) generated from hisat2-2.2.0 pipeline, a reference fasta file and fastq file of MinION. Please let me know the command to RUN RSEM to analysis my data.

[bli25]

@sekhwal , unfortunately, RSEM does not handle MinION data right now.

[sekhwal]

Is there any other way to handle data similar to RSEM for MinION?

[sekhwal]

I have Illumina sequencing fasta files also. Could you please let me know how to install and RUN RSEM?