Struggling to get started

[inti]

Hi, I am finding difficult to get started with emase-zero. I am following this protocol suggested on the webpage

$ bowtie -q -a --best --strata --sam -v 3 -m 100 bowtie.transcriptome my_sample.fastq | samtools view -bS - > my_sample.bam
$ alntools bam2ec -t transcripts.lengths.tsv -c 8 my_sample.bam my_sample.bin
$ emase-zero -m 2 -b my_sample.bin -o emase-zero.quantified -l transcript.lengths.tsv -g gene2transcripts.tsv

My doubts are:

• where does the bowtie.transcriptome file comes from? is it bowtie index for the reference transcriptome or is it for a personalised transcriptome?
• do I need to do I incorporate a vcf with known genetic variation for each individual? to make the a personalised transcriptome, i.e., bowtie.transcriptome used in the first step?

Do you have working example with some test files that I could follow? Thanks a lot in advance.

Regards,

Inti

[inti]

I think I have sorted myself out. thanks!