I have DNA Sanger sequence FASTA files from patient TGM1 genes, and have been trying to use subread to align them to the TGM1 coding reference sequence from NCBI.
I keep getting a weird red looking .sam file as the result from the alignment but it doesn't look correct at all. I've attached here: weird .sam file
So far the code I've used has been:
subread-buildindex -o TGM1_index /home/amyhouseman/Desktop/fasta_reference_TGM1_folder/TGM1_ref_sequence
subread-align -t 1 -i TGM1_index -r /home/amyhouseman/Desktop/katja_fasta_seq/fasta_trimmed_sequences/fasta_trimmed_1_all/fasta_trimmed_1_final.fasta -o my_results.sam
This doesn't look right to me, so I was wondering if anyone has seen an error like this before? My DNA sequences are only around 500bp, and I only used one to map with, so i could check if it worked before using all 42 of them.
Thanks! Amy *This is on Ubuntu terminal