A question of samtools

[littlebio]

Hi, I'm new in this field, there is one problem I want to ask

I have already sorted and index the .sam file, and it changed to .bam.bai file
I want to check the result of .bam.bai file, but I don't know use which of samtools command. I want to view them in a .map file.

Thanks

[nilshomer]

Hi, I'm new in this field, there is one problem I want to ask

I have already sorted and index the .sam file, and it changed to .bam.bai file
I want to check the result of .bam.bai file, but I don't know use which of samtools command. I want to view them in a .map file.

Thanks

Please don't post the same question twice in multiple threads, since then it gets difficult to respond.

Anyhow, you should have an associated BAM file with your BAI file. The BAI file is an index of your BAM file. I am not sure of a BAM to .map converter, though I would ask why you need a .map file. Many genome browsers like IGV work well with BAM files and variant callers like the one in samtools or GATK also play nice with BAM files.

[littlebio]

Please don't post the same question twice in multiple threads, since then it gets difficult to respond.

Anyhow, you should have an associated BAM file with your BAI file. The BAI file is an index of your BAM file. I am not sure of a BAM to .map converter, though I would ask why you need a .map file. Many genome browsers like IGV work well with BAM files and variant callers like the one in samtools or GATK also play nice with BAM files.

Sorry for posting twice, and thanks for your reply.

I saw another result that the output is a MAP file, so I think maybe it is easy to output that way. Actually, I only want to see the result of BAI file, no matter what kind of output. And I tried the command:
samtools view XXXXX.bam.bai
it did not work, so I want to know how to convert this file correctly.

Thank you

[nilshomer]

Sorry for posting twice, and thanks for your reply.

I saw another result that the output is a MAP file, so I think maybe it is easy to output that way. Actually, I only want to see the result of BAI file, no matter what kind of output. And I tried the command:
samtools view XXXXX.bam.bai
it did not work, so I want to know how to convert this file correctly.

Thank you

The command you want is:

samtools view XXXXX.bam

The .bai file does not store your alignments, the .bam file does.

[nilshomer]

Sorry for posting twice, and thanks for your reply.

I saw another result that the output is a MAP file, so I think maybe it is easy to output that way. Actually, I only want to see the result of BAI file, no matter what kind of output. And I tried the command:
samtools view XXXXX.bam.bai
it did not work, so I want to know how to convert this file correctly.

Thank you

Also, you might want to list the commands you used starting at the .sam file. The commands:

samtools sort XXXXX.sam XXXXX
samtools index XXXXX.bam

should produce a .bam file (stores your alignment) and .bai file (index of your .bam file, for fast co-ordinate retrieval).

[littlebio]

Thank you for your suggestion, I have already worked out.