Hi, I use bowtie2-2.2.9 to align Fasta reads with some genes. I don't know I understand correctly end-to-end alignment in Bowtie2 or not. Based on my understanding if we have a read same as bellow:
And we use end-to-end (it seems default option) in our alignment the aligning should involves all the characters in the read. But in my result I have some local aligning. Same as bellow that just use 8 character of read in alignment.
Read1 16 Gene.1 19 1 8M * 0 0 TAAAAAAA IIIIIIII AS:i:0 X
I run the Bowtie command with these options:
bowtie2 -f -x RefGene -U merged.fasta -S output.txt -p 6 --no-hd --no-sq --no-unal
Also I am sure that the length of Read1 is longer than 8. It is 88. I am wondering if I need to add any option in running bowtie2 to force it to align end-to-end?