[maubp]

Some mapping software does not report unmapped reads in the SAM/BAM output (or can do this optionally), or your pipeline may have dropped them. So it may be expected that the final row (with the *) is all zeros.

If you are asking why the fourth column is zero, that is typically the unmapped partners of paired reads which did map to that reference sequence. This relies on the mapper following SAM/BAM best practice which also ensures the unmapped partner reads are near by their mapped partner when the file is sorted by coordinate.

If you have single end reads, then the fourth column should be all zeros.

[Gonza]

that make sense, it is a single end RNAseq experiment. Thanks.
G

[dena.dinesh]

In my case I have used paired-end reads and that has benn mapped using bowtie2 to a transcriptome and has been sorted and the reads were conuted using samtools idxstats.

For my bam files the fourth column has value 0 for all the transcripts and while the last line of has * 0 0 4707222.

Is there anything wrong in my data?

[maubp]

Hi dena.dinesh. Maybe you were lucky and all your paired reads mapped nicely. However, my guess is the unmapped partners have simply all been counted in the final line (rather than against the reference of their mapped partner in column four).

You could try using "samtools fixmate" (or the Picard equivalent) on the BAM file and then reindex and repeat "samtools idxstats".