I am new to bioinformatics and I am following a de novo transcriptom assembly workflow. I have about 20 paired end fastq files (10*2 files). The assembly has finished and I got a Trinity.fasta as output. I am now working on a susbset of interested transcripts in a fasta file : subset.fasta.
What I did is running a bowtie2 (using my reads and subset.fasta) and now I have 10 .bam files associated. I have checked some tools like HTseq but I am honestly lost in the documentation.
Does anyone know an easy ro reach my goal from there (the number of reads mapping each transcript of subset.fasta for each of my 10 samples) ?
Thank you for your support !