differences between gtf file and indexing file (hg19)

[rozitaa]

Hi,

Sorry for asking so simple questions but I am new in bioinformatics. I have some mouse RNA-seq data and I would like to align them by TopHat. I know a bit about gtf file (representing position of genes) and indexing or annotating file (e.g. hg19 or mm10) (representing function of genes). I was wondering if I am right! and if there would more information about them!
I was also wondering about library type of reads (stranded or unstranded)! and if they both work for single-end or paired-end sequences.

Thanks

[dpryan]

Well, a GTF file would be an annotation of the genome, describing where features are and their structure. Functions could be added to an annotation file, but are often in a separate file, which wouldn't really be an annotation since they often lack genomic locations (using gene or transcript names instead, for example). Indexing is a generic term that can apply to a lot of things. For example, genome annotations are indexed by genomic coordinate. A file describing gene ontology might be indexed by gene or ontology category. Alternatively, genomes themselves can be indexed to make alignment faster. That term doesn't have any particular definition aside from that used in English.

Stranded-ness of library preparation is separate from whether the library is subsequently sequenced with single or paired-ends.