Bowtie2

[winsettz]

bowtie isn't a normal command with bowtie2. Are you keeping bowtie in your PATH along with bowtie2?

If you build your ebwt in the /examples/reference directory

bowtie2-build lambda_virus.fa lambda_virus

Then run the example in the reference directory

bowtie2 -x lambda_virus -U ../reads/reads_1.fq -S eg1.sam

Output is:

10000 reads; of these:
10000 (100.00%) were unpaired; of these:
596 (5.96%) aligned 0 times
9404 (94.04%) aligned exactly 1 time
0 (0.00%) aligned >1 times
94.04% overall alignment rate

Did you use bowtie-build or bowtie2-build? Don't have a copy of bowtie anymore (switched over to bowtie2), so I can't say if bowtie and bowtie2 indexes are compatible. Pretty sure they aren't, but I can't test it in front of me.

If you built with bowtie-build instead of bowtie2-build, it /might/ be the problem.

[Layal]

Hello,

I tried to work with bowtie2 under Linux, but I faced many problems:
1- The command (bowtie2) is not working as it's written in the manual of Bowtie 2 package but normal commands as bowtie and bowtie build are working.
2- the example which is with the package lambda_virus , the basename is not recognized although the index files have this basename, so no alignment is allowed, I tried to build other indexes for other genome and set new basename by bowtie builder, but again the new basename is not recognized by bowtie2
I use the same commands with bowtie1 without any problems so far.

Thanks,
Layal