RNA alignment by Hisat2

Question

[vaishali.pankaj124]

Is this the sam output file generated after hisat2?

@HD     VN:1.0  SO:unsorted
@SQ     SN:NC_016407.2  LN:52991155
@SQ     SN:NC_016408.2  LN:45729672
@SQ     SN:NC_016409.2  LN:55515152
@SQ     SN:NC_016410.2  LN:56582383
@SQ     SN:NC_016411.2  LN:43630510
@SQ     SN:NC_016412.2  LN:35275713
@SQ     SN:NC_016413.2  LN:49172423
@SQ     SN:NC_016414.2  LN:45569985
@SQ     SN:NW_013657548.1       LN:525692

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Furthermore, you posted this as a "Tutorial" post type, while this is obviously a question. I changed the post type.

Answer 1

[WouterDeCoster]

What you are looking at is the SAM/BAM header. See the specifications. The sequence alignment is a bit lower in the file, below the header lines.