mapping transcriptome to genome to find TSS/TES/(+/-)
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?
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