Do I need to create an index for my reference genome?

[wmseq]

Hi every one,
After I aligned the reads of my samples with tophat, do I need to to create an index for my reference genome like after bowtie2 alignment, and then convert/sort/index all my sam files to identify the upregulated and down-regulated genes from a compound treatment?
Thanks a lot!!
Richard

[dpryan]

No, you don't need to do that.

[wmseq]

Thank you, dpryan!!
Do I need to convert/sort/index all my sam files, because I saw a question on a problem with unsorted bam files for HTSeq-count?

[dariober]

Thank you, dpryan!!
Do I need to convert/sort/index all my sam files, because I saw a question on a problem with unsorted bam files for HTSeq-count?

From my memory I recall tophat produces bam files sorted by position. htseq-count needs sam files sorted by read name only if the reads are paired-end. If they are single end I don't think the order matters.

[wmseq]

But I read a tutorial, it seams that all sam files should be convert/sort/indexed. I am not sure.

[dpryan]

If you have paired end reads, then you need to name sort the file (usually you would sort a BAM file, rather than a SAM file). There's no need to create an index when using htseq-count, it will ignore it.