Problem about samtools sort and tview, Who can help me?

[[email protected]]

Hello everyboday, I am a newbie, my sam file size is about 45,786 kB, however after I use the samtools sort command, the .bai file produced is just only 1 kb, I wander it is right. In addition, after I use the samtools tview command, the result show a line N and nothing. I don't know where the problem is, who can help me?

[aprice67]

Samtools sort will produce a sorted bam file and a .bam.bai file to go with it.

For example,
samtools sort bam_unsorted.bam > myBam_sorted.bam

That will make: myBam_sorted.bam and myBam_sorted.bam.bai, and the .bam.bai file will be small.

Also consider if you want to sort by position or by name, many things require by name, especially when working with paired end data, you'd need to include the -n option in samtools sort for that.

Good luck.

[[email protected]]

Samtools sort will produce a sorted bam file and a .bam.bai file to go with it.

For example,
samtools sort bam_unsorted.bam > myBam_sorted.bam

That will make: myBam_sorted.bam and myBam_sorted.bam.bai, and the .bam.bai file will be small.

Also consider if you want to sort by position or by name, many things require by name, especially when working with paired end data, you'd need to include the -n option in samtools sort for that.

Good luck.

To: aprice67
thank you for your reply.
Yes, I have soted my bam file, thne made samtools index and got bai file, the bai file is just 1kb.
after then I use the command: samtools tview sorted.bam reference.fas
the result is as following, while not be the sequence. so I don't which step is wrong.

[GenoMax]

It is normal for the .bai file to be small (compared to the bam file). It only contains index values that indicate where particular regions (chromosomes in this case) start in the bam files.

Ends of chromosomes contain unsequenceable hetero-chromatin, which is represented by the N's that you are seeing. If you keep scrolling to the right or jump to a different location you should be able to see sequence/reads.

I suggest that you give IGV a try as a graphical viewer with your reference/bam/bai files.