Tophat & IGV viewing

Question

[aleka]

Hi, I got the accepted_hits.bam from tophat, I created the index with samtools and then I created in IGV a genome using the reference fasta and gtf file for my species (staphylococcus aureus) and once I load the accepted_hits.bam file, IGV gives me an error.

Any idea why?

[Brian Bushnell]

It certainly wouldn't hurt to post the error message.

[marongiu.luigi]

I got exactly the same kind of error, which is the standard "Could not load index file for: /media/gigiux/float_ngs/mtb/samp1/accepted_hits.bam An index file is required for SAM & BAM files". Aleka, did you get any feedback on this issue?

[marongiu.luigi]

A reason why IGV does not open the accepted_hits.bam might be that it has to be indexed with samtools first, as I have found out in this link. What are the command lines to do that I don't know yet...

[marongiu.luigi]

The way I did is goes like this. Mapping on IGV requires the creation of sorted and indexed files with samtools (sort gives the .bam extension automatically; index creates a .bam.bai file that works as reference for the .bam; both .bam and .bam.bai need to have the same root name; IGV loads the .bam but then uses the .bam.bai internally):

samtools sort <accepted_hits.bam> <sort>
samtools index <sort.bam>

[Shicheng Guo]

Hi Aleka, Where to download GTF file for Staphylococcus aureus? Thanks.