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Hello, I am currently trying to align two closely related genomes from multiple sequence fasta files. I have a target genome which is made of 1168 sequences in a single fasta file and I wish to use this to build indexes. Initially I did this with the command "bowtie-build target_file.fa t_index". This ran in a reasonable amount of time and produced 6 index files: t_index.1.ebwt, t_index.2.ebwt, t_index.3.ebwt, t_index.4.ebwt, t_index.rev.1.ebwt, t_index.rev.2.ebwt.
I then ran the command "bowtie t_index -f -t -p4 -l 13 ../PATH/TO/QUERY output.map" to run an alignment, where QUERY is also a multiple sequence fasta file where each sequence length is <= 1024 bases. My output was not what I was expecting; I got only 5.03% alignment when I was expecting over 90%. This lead my to wonder whether or not indexes had been created correctly. Is bowtie-build able to take a multisequence fasta file? Maybe each index file was being overwritten by each following sequence in the target file? I tweaked some parameters and was still not able to get over 6% alignment.
I then ran the command "bowtie t_index -f -t -p4 -l 13 ../PATH/TO/QUERY output.map" to run an alignment, where QUERY is also a multiple sequence fasta file where each sequence length is <= 1024 bases. My output was not what I was expecting; I got only 5.03% alignment when I was expecting over 90%. This lead my to wonder whether or not indexes had been created correctly. Is bowtie-build able to take a multisequence fasta file? Maybe each index file was being overwritten by each following sequence in the target file? I tweaked some parameters and was still not able to get over 6% alignment.
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