I'm new to Galaxy and bioinformatics tool.
I have Fastq data of chicken heavy and light chains and I want to do pca plot on them. I know I have to convert them to BAM file first but I don't know which tool to use - FastqtoSam or Bowtie2. One gave me unaligned BAM and another gave aligned BAM. Then, I used multiBAMsummary tool to see which file was correct but both BAM file gave me an error saying file '0.bam' does not have BAM or CRAM format.
Where did I go wrong?