Are the BAM files from tophat and bowtie-samtools the same?

Question

[jolin0701-dy]

I know we can get accepted_hits.bam from tophat like this:

tophat2 --max-multihits 1 --b2-very-sensitive --GTF mm10.gtf --output-dir CZ-1_thout genome CZ1.fastq

And I know we can also get a bam file from bowtie-samtools pipeline like this:

bowtie2 -q -x genome -U CZ1.fastq -S CZ1.sam

samtools view -Sb CZ1.sam> CZ1_nonSorted.bam

samtools sort -o CZ1.bam CZ1_nonSorted.bam

samtools index CZ1.bam

So my questions is what is the difference between these bam files?

Thanks so much~~

[GenoMax]

BAM file format is a published specification. All files purporting to be in that format must adhere to fields that are minimally required.
So the difference in the files would be the differences in mapping (if applicable) but format wise they should be BAM's.

Answer 1

[igor]

TopHat takes exon boundaries into account (this is why you give it a GTF file). Bowtie does not.

The TopHat website summarizes the difference:

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

More generally, any aligner will give you a BAM file. They will all be different.

[John]

"any aligner will give you a BAM file. They will all be different."

Amen