Why am I able to open BAM file in text editor?

Question

[Joshua]

I ran into an odd situation where I'm able to open bam file in text editor..... I know it sounds strange!!!

I'm working with mitochondrial genome, and I had to filter out reads that are aligning only to mitochondrial reference genome (I'm using revised Cambridge reference sequence (NC_012920)). However, the resulting bam file is not in compressed format. The file extension is in .bam, but, I'm able to open it in a text editor.

Here are the steps how I got to this bam file.

#I'm using hisat2 to align fastq file to mitochondrial reference genome (I indexed it with hisat2).
hisat2 -p 8 -x /home/user/Reference_genome/mitochondria/chrM -1 /home/user/mitochondrial_analysis/SRR6423582_R1.fastq.gz -2 /home/user/mitochondrial_analysis/SRR6423582_R2.fastq.gz > /home/user/mitochondrial_analysis/SRR6423582.sam

#Converting SAM to BAM. (In this step BAM is getting generated properly in compressed format....)
samtools view -h -S -b /home/user/mitochondrial_analysis/SRR6423582.sam > /home/user/mitochondrial_analysis/SRR6423582.bam

#Sorting BAM file. (BAM file is in correct format here as well..)
samtools sort /home/user/mitochondrial_analysis/SRR6423582.bam -o /home/user/mitochondrial_analysis/SRR6423582_sorted.bam

#Filtering out reads aligned only to mitochondrial genome. (Only in this last step, the generated BAM file is not in compressed format.) 
samtools view -f 0x3 /home/user/mitochondrial_analysis/SRR6423582_sorted.bam > /home/user/mitochondrial_analysis/SRR6423582_MT.bam

First, I assumed, since the file size is less, samtool has not compressed it. However, when I tried to parse this bam file to another tool, it's throwing as exception stating SAMFormatException: Does not seem like a BAM file. Could someone please help me with this issue?

Also, I would like to mention that this is my first project with mitochondrial genome. So, if I'm making any mistakes in the previous steps, please correct me.

Answer 1

[Pierre Lindenbaum]

it's not a BAM, it's a SAM file. I'm just surprised that you found a SAM header with the command:

samtools view -f 0x3 /home/user/mitochondrial_analysis/SRR6423582_sorted.bam > /home/user/mitochondrial_analysis/SRR6423582_MT.bam

to get a BAM file, you want something like:

samtools view -O BAM -f 0x3 /home/user/mitochondrial_analysis/SRR6423582_sorted.bam > /home/user/mitochondrial_analysis/SRR6423582_MT.bam

[Joshua]

Thank you for guiding me @Pierre Lindenbaum. I'm able to get BAM file correctly now. :)

[Joe]

As a general note in case this wasn't obvious - file extensions in Unix systems are merely conventions, they don't actually "mean" anything. Just because it ends in .bam doesn't guarantee anything about the file content.