I should work with Rseq data with bowtie2
I tried these steps but at last it says "bowtie2-builds exe is not recognized as an external or internal and operable command or batch file"
I cried a lot because its too difficult accepting this reality that im a stupid and I should change my route in life from bioinformatics to something else…
I tried windows 8
Even I tired tdm gcc as compiler and mingw.org but in between I got confused
Step 1) Download this package: http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.4/bowtie2-2.2.4-mingw-win64.zip/download
Step 2) Unzip it. Place it in a folder you can navigate to, something simple, such as C:\bowtie2_win64
Step 3) Assuming you have windows 7 (you should say what operating system you are using), open "cmd.exe", this is command prompt, you can open it by pressing WindowsKey+R and typing cmd.exe + enter
Step 4) In command prompt (black windows), navigate to where you have unzipped your bowtie, in Step2 I told you to put it in C:\bowtie2_win64, so write in command prompt "cd C:\bowtie2_win64".
Now you need to test whether the precompiled windows binary works for you, so:
Step 5) Index example fasta file, type "bowtie2-build-s.exe example/reference/lambda_virus.fa lambda_virus
Step 6) If all goes well, next you need to align the sample reads provided "bowtie2-align-s.exe -x lambda_virus -U example/reads/reads_1.fq -S eg1.sam"
If all went well, you should see:
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