I would like to annotate sequences from single-end fastq files (225bp length) with regards to Line1 structure. i.e. Orf1/Orf2
I tried aligning the fastq files and then doing annotation (TEtranscript), but since I only have 500 to 1000 reads total this approach failed. The reads were not alligned to the genome even when permitting -k 5000 with bowtie2.
I would greatly appreciate tips regarding short read annotation of short-read fastq sequences.
Example of sequence: AGAGAATCTCAGGTGCAGAAGATTCCATAGAGGACATCGACACAACAGTCAAAGAAAATACAAAATGCAAAAGGATCCTAACTCAAAACATCCAGGTAATCCAGGACACAATGAGAAGACCAAACCTACGGATAATAGGAATTGATGAGAATGAAGATTTTCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATATCTCGTATGCCGTCTTC
I also tried L1base and looking into repeatblast - but not sure if this would be a suitable approach.
I hope this somewhat makes sense since I am also new to this.