TopHat output

[rururara]

I run bowtie - top hat with my 91bp paired end reads.
There's supposed to be accepted_hits.sam as an output file.
but I got accepted_hits.bam.
i'm a little bit confuse here.
i run this command 'tophat -r <parameter> <ref base name> <reads1> <reads2>'
anyone experienced with that?
thanks!

[dnusol]

Hi,

that happened to me too. I think the manual is outdated. BAM files are generated which can be directly used in cufflinks for example.
If needed you can transform BAM to SAM with samtools

HTH,

D.

[rururara]

ok. that means 'that' .BAM file is used for cufflinks program.
so if i want to use it for another program i have to convert into SAM. isn't?
thanks anyway!

[Jon_Keats]

most programs will that accept .sam files will take the binary .bam version (ie. the bam format is really just a compressed, to save disk space, version of a sam file)

[rururara]

i did the same thing but still can't visualize my alignment.
unless i index the bam file then won't take the big space.
however IGV doesn't accept .bam.bai format.

[Jon_Keats]

to view in IGV you need the .bam file and the indexed .bam.bai file in the same folder. Then in IGV load the .bam file after selecting the appropriate genome. The bai file is an index file used to speed up navigation and queries from IGV on the .bam file.

[Emilie]

Hi,
If you need the sam file, you can also use the --keep-tmp option when running TopHat.
In the manual on TopHat website: "--keep-tmp : Causes TopHat to preserve its intermediate files produced during the run. By default, they are deleted upon exit."
Emilie