View BAM file

[syintel87]

When I see a BAM file by running the command, "samfile view -h accepted_hits.bam",
the result is like the attachment.

My quetion is,
"Is it okay for the rows from Contig0 to Contig9 to have shorter space ahead of LN than the rows from Contig10 to the end do have?"

Thank you in advance.

[xied75]

That is not SPACE, but TAB.

[avilella]

It's a column-based format separated by tabs. For visualization purposes, if you want to pipe the tab-separated columns into something that looks pretty on the screen, in Linux you can use 'column -t' like this (notice only first 100 lines):

samfile view -h accepted_hits.bam | head -n 100 | column -s $'\t' -t | less

[syintel87]

It's a column-based format separated by tabs. For visualization purposes, if you want to pipe the tab-separated columns into something that looks pretty on the screen, in Linux you can use 'column -t' like this (notice only first 100 lines):

samfile view -h accepted_hits.bam | head -n 100 | column -s $'\t' -t | less

Oh, thank you very much!