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? 



That means it did not run. You can align the fastq files using `bowtie2`:

    bowtie2  -x index -1 R1.fastq -2 R2.fastq -S bowtie.sam

Then convert the `sam` to `bam` using `samtools`:

    samtools view -bS bowtie.sam -o bowtie.bam

Then `sort` it:

    samtools sort bowtie.bam -o bowtie.sorted.bam

You can `index` the `.sorted.bam` by using:

    samtools index bowtie.sorted.bam