I have a transcriptome fasta file that looks like this:
>loc.00001.1 gene=loc.00001 TCATTTTCCTGGCATGGATAATTTCGCTGCAAAAGGTGTCGCACCTGAAACAGGAGAAATGCATTAGCAG CTGTCAAATTACCACGAATTTCGGAGATTATGACGACATTTTAGAATGCGACCAATCGAAACTCGAATCG AGAAATCTCTATGAGATATTTTCATTTCTCACATTGATAACGGGAATCGAGGAATTCCATGAGCAGAACA TTTGGATTAAATGCTTTCACGATTTGGTGACCGATTTCATCATCTACATGCCGAAAAGGCTCAAGGATTT
I also have a genome fasta file that is around -500 contigs long.
> contig_1 attgacaatttaactcgagcattgttctcgtttacataacattatctcatatgtcctttaccacatctttgtagtttttctggctactcctgggataat
I want to map the transcriptome to the genome such that I can produce a resultant bed file that has the transcript ID, contig ID, TSS, TES, and +/- orientation?
Would I have to use a program like gmap? Would that give me the information I need?