[B]Bowtie and Samtools questions[/B]

[dicty]

I'm new in sequencing analysis and have a couple of questions to ask.

1. I’m trying to use bowtie-inspect to reconstruct fasta file from the BOWTIE index, but couldn’t get anything. I’m using 12.7 version.

Here is the command:
./bowtie-inspect e_coli

Then I got the following output, but nothing else:
Command: ./bowtie-inspect e_coli

Why I cannot run bowtie-inspect? Is there anything wrong?

2. I installed samtools and try to produce a .fai file with "samtools faidx", but I got the following errors.

./samtools: No such file or directory
or
samtools: command not found

How do I run samtools? Is there anything wrong I did?

Thanks a lot!

[epigen]

include the path

If you haven't included the path to your program in your PATH variable, and you're in a different directory (folder) than the one your program resides in, you'll have to call it using the full path to the location you have installed them in, something as
/home/yourname/programs/bowtie/bin/bowtie-inspect e_coli

[marcora]

If you haven't included the path to your program in your PATH variable, and you're in a different directory (folder) than the one your program resides in, you'll have to call it using the full path to the location you have installed them in, something as
/home/yourname/programs/bowtie/bin/bowtie-inspect e_coli

The above is a good suggestion to solve your samtools problem. However, it doesn't apply to your with your bowtie-inspect problem (the system can find the executable just fine).

The problem there is that you will have to supply the full path to the directory where the bowtie index resides (I think this is a bug in the most recent version of bowtie, it did not require this before, which makes more sense since bowtie should know where its indexes are).

Therefore you should try:

bowtie-inspect PATH_WHERE_ECOLI_EBWT_FILES_RESIDES/e_coli > e_coli.fa

and voitla, you should have your e_coli.fa reference genome in fasta format!

[dicty]

Yes, it works. Thanks a lot for the suggestions!