how to use samtools to open my bam file

[wangli]

I am a very beginner in using samtools.
I tried "samtools view myfile.bam" in the desired directory. It didnot work.
Thanks!

[wangli]

samtools view -H INX730_D0AJWACXX_6_AAACAT.bam
bash: samtools: command not found

I installed samtools as suggestions here:

wget http://sourceforge.net/projects/bio-...r.bz2/download
wget http://sourceforge.net/projects/samt...r.bz2/download
tar -jxf bwa-0.5.5.tar.bz2; tar -jxf samtools-0.1.7a.tar.bz2
(cd bwa-0.5.5; make; cp bwa $HOME/bin)
(cd samtools-0.1.7a; make; cp samtools misc/samtools.pl $HOME/bin)
export PATH="$PATH:$HOME/bin" # this is bash only.

when doing command as cp samtools misc/samtools.pl /usr/bin
only samtools.pl can be copied.

I appreciate any help. Thanks!

[dpryan]

samtools view -H INX730_D0AJWACXX_6_AAACAT.bam
bash: samtools: command not found

(cd samtools-0.1.7a; make; cp samtools misc/samtools.pl $HOME/bin)
export PATH="$PATH:$HOME/bin" # this is bash only.

when doing command as cp samtools misc/samtools.pl /usr/bin
only samtools.pl can be copied.

I appreciate any help. Thanks!

If the samtools executable isn't copied properly, as you suggested, then that's probably the problem. If you get an error when you copy the executable then it'd be helpful if you provided it.

[wangli]

I go to the samtools-0.1.8 directory, and didnot find the executable "samtools", except a file named as samtools.1, which explains the usage of samtool command.
My version is 0.1.8.
I could not find the executable file.

[dpryan]

Then something borked during compilation. Type "make clean && make" (without the quotes) in that directory and post whatever error you eventually get. Of course, you could get lucky and it works properly in compiling the executable. In that case, copy it into your PATH and proceed with usage.

[wangli]

I go to the samtools-0.1.8 directory, and didnot find the executable "samtools", except a file named as samtools.1, which explains the usage of samtool command.
My version is 0.1.8.
I could not find the executable file.

when I do make, I run into the following problems:
bam_tview.c:5:20: error: curses.h: No such file or directory
bam_tview.c:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
bam_tview.c:434:2: warning: #warning "No curses library is available; tview is disabled."
make: *** [bam_tview.o] Error 1

Thanks!

[dpryan]

Then either install ncurses or follow the INSTALL document:

The text-based viewer (tview) requires the GNU ncurses library
<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
the modern Linux/Unix distributions. If you do not have this library installed,
you can still compile the rest of SAMtools by manually changing:
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='.

[wangli]

Oh, great! Thanks a lot!
I have make it.