Dear all,

I have this instruction:

1. Format the database of 890 Clarias specific genes (Clarias-specific DB)
2. Download the Clarias genome reads from NCBI (all reads, not assembly)
3. Align Clarias genomic reads to Clarias-specific DB
4. Download zebrafish genomic reads from NCBI
5. Align zebrafish genome reads to Clarias-specific DB
6. Summarize the number of aligned Clarias vs. zebrafish reads for each gene.
7. Let me know the location of BAM files and summary table

But I have a few questions about that, if it means I will easily make a database for 890 Clarias specific genes, and then align the Clarias genome reads as well as the zebrafish genome reads to that DB, respectively? But if that is correct, the output will be a blastout file, where could I find the BAM files? And here is the command I used:

makeblastdb -in clarias_specific_seq.fasta -dbtype 'nucl' -hash_index -parse_seqids -out clarias_speficic_db

blastn -query SRR11188_1.fastq -db clarias_speficic_db -evalue 1e-5 -num_threads 20 -max_target_seqs 60 -outfmt 6 -out cl_cl_SRR11188_1.blastout

And if my understanding is wrong, if I need to use Bowtie or Hisat2 to finish this instruction? Which also need the genome gtf file etc....

I am pretty confused about this and will be appreciated if you could give some instructions..