[zillur]

Thank you very much. I have typed "make" in the directory. Now my files are

Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ ls
AUTHORS bam_plbuf.c faidx.c
ChangeLog.old bam_plbuf.h faidx.o
INSTALL bam_plbuf.o htslib-1.1
LICENSE bam_plcmd.c kaln.c
Makefile bam_plcmd.o kaln.h
Makefile.mingw bam_reheader.c kaln.o
NEWS bam_reheader.o kprobaln.c
README bam_rmdup.c kprobaln.h
bam.c bam_rmdup.o kprobaln.o
bam.h bam_rmdupse.c libbam.a
bam.o bam_rmdupse.o libhts.a
bam2bcf.c bam_sort.c misc
bam2bcf.h bam_sort.o padding.c
bam2bcf.o bam_split.c padding.o
bam2bcf_indel.c bam_split.o phase.c
bam2bcf_indel.o bam_stat.c phase.o
bam2depth.c bam_stat.o sam.c
bam2depth.o bam_tview.c sam.h
bam_aux.c bam_tview.h sam.o
bam_aux.o bam_tview.o sam_header.c
bam_cat.c bam_tview_curses.c sam_header.h
bam_cat.o bam_tview_curses.o sam_header.o
bam_color.c bam_tview_html.c sam_view.c
bam_color.o bam_tview_html.o sam_view.o
bam_endian.h bamshuf.c sample.c
bam_flags.c bamshuf.o sample.h
bam_flags.o bamtk.c sample.o
bam_import.c bamtk.o samtools
bam_import.o bedcov.c samtools.1
bam_index.c bedcov.o samtools.h
bam_index.o bedidx.c stats.c
bam_lpileup.c bedidx.o stats.o
bam_lpileup.h cut_target.c stats_isize.c
bam_lpileup.o cut_target.o stats_isize.h
bam_mate.c errmod.c stats_isize.o
bam_mate.o errmod.h test
bam_md.c errmod.o version.h
bam_md.o examples win32
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ make
make: Nothing to be done for `all'.

Is it compiled now? What should i do next?

Regards
Zillur

[GenoMax]

Looks like the compilation is done. Can you run the samtools executable like so

$ samtools-1.1/samtools

That should print some help messages.

[zillur]

Thank you very much. Yes, I think its working now.

Mds-MacBook-Pro:samtools ZILLURRAHMAN$ samtools-1.1/samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.1 (using htslib 1.1)

Usage: samtools <command> [options]

Commands:
-- indexing
faidx index/extract FASTA
index index alignment
-- editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
rmdup remove PCR duplicates
targetcut cut fosmid regions (for fosmid pool only)
-- file operations
bamshuf shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
bam2fq converts a BAM to a FASTQ
-- stats
bedcov read depth per BED region
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion

Mds-MacBook-Pro:samtools ZILLURRAHMAN$
What next? I aligned the example lambda virus. Now I want to convert the sam file into bam file and then using flagstat I have to assess the quality of the alignments.

Regards
Zillur

[GenoMax]

What next? I aligned the example lambda virus. Now I want to convert the sam file into bam file and then using flagstat I have to assess the quality of the alignments.

Regards
Zillur

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#using-samtoolsbcftools-downstream

[zillur]

Thank you very much. I am using these following command lines. But:-
upr189081:reference ZILLURRAHMAN$ $BT2_HOME/bowtie2 -x $BT2_HOME/example/index/lambda_virus -1 $BT2_HOME/example/reads/reads_1.fq -2 $BT2_HOME/example/reads/reads_2.fq -S eg2.sam
-bash: /bowtie2: No such file or directory
upr189081:reference ZILLURRAHMAN$

What should I do now?

[GenoMax]

What is $BT2_HOME set to? Is bowtie2 in $BT2_HOME directory?

[zillur]

I don't know. Here is my directory.
upr189081:~ ZILLURRAHMAN$ cd desktop/bioinformatics/bow-tie/bowtie2-2.2.3/example/

[GenoMax]

$BT2_HOME designates a variable that you need to set, before you can use it in a command line.

$ export BT2_HOME=/path_to/desktop/bioinformatics/bow-tie/bowtie2-2.2.3

Replace the path_to part with real full path.

[zillur]

Thank you very much. Here is my bash profile. I have tried. But.....May be I am missing something....

upr189081:~ ZILLURRAHMAN$ open ~/.bash_profile
upr189081:~ ZILLURRAHMAN$ open ~/.bash_profile
upr189081:~ ZILLURRAHMAN$ cd desktop/bioinformatics/bow-tie/bowtie2-2.2.3/example/
upr189081:example ZILLURRAHMAN$ $BT2_HOME/bowtie2 -x $BT2_HOME/example/index/lambda_virus -1 $BT2_HOME/example/reads/reads_1.fq -2 $BT2_HOME/example/reads/reads_2.fq -S eg2.sam
-bash: /bowtie2: No such file or directory
upr189081:example ZILLURRAHMAN$ cat ~/.bash_profile
export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/Bow-tie/bowtie2-2.2.3/:$PATH"
export PATH=“users/ZILLURRAHMAN/desktop/bioinformatics/bow-tie/bowtie2-2.2.3/BT2_HOME:$PATH”
upr189081:example ZILLURRAHMAN$ cd
upr189081:~ ZILLURRAHMAN$ open ~/.bash_profile
upr189081:~ ZILLURRAHMAN$ $BT2_HOME/bowtie2 -x $BT2_HOME/example/index/lambda_virus -1 $BT2_HOME/example/reads/reads_1.fq -2 $BT2_HOME/example/reads/reads_2.fq -S eg2.sam
-bash: /bowtie2: No such file or directory
upr189081:~ ZILLURRAHMAN$ cat ~/.bash_profile
export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/Bow-tie/bowtie2-2.2.3/:$PATH"
export PATH=“users/ZILLURRAHMAN/desktop/bioinformatics/bow-tie/bowtie2-2.2.3/BT2_HOME:$PATH”
$ export BT2_HOME=/path_to/desktop/bioinformatics/bow-tie/bowtie2-2.2.3
upr189081:~ ZILLURRAHMAN$

[GenoMax]

At this point try following.

$ cd desktop/bioinformatics/bow-tie/bowtie2-2.2.3

$ bowtie2 -x example/index/lambda_virus -1 example/reads/reads_1.fq -2 example/reads/reads_2.fq -S eg2.sam

You really need to go back and understand the concept of relative paths, working directories (this info is included in the Korf lab unix course I had pointed you to).

[zillur]

Hi,
Thank you very much. Here I got an unusual problem. In my terminal basic commands are not found like:

mds-macbook-pro:~ ZILLURRAHMAN$ ls
-bash: ls: command not found
mds-macbook-pro:~ ZILLURRAHMAN$ env
-bash: env: command not found
mds-macbook-pro:~ ZILLURRAHMAN$ edit
-bash: edit: command not found
mds-macbook-pro:~ ZILLURRAHMAN$ open
-bash: open: command not found
mds-macbook-pro:~ ZILLURRAHMAN$ vi
-bash: vi: command not found
mds-macbook-pro:~ ZILLURRAHMAN$ tail
-bash: tail: command not found
mds-macbook-pro:~ ZILLURRAHMAN$ ls
-bash: ls: command not found
But echo is working. Like: mds-macbook-pro:~ ZILLURRAHMAN$ echo $PATH
“users/ZILLURRAHMAN/desktop/bioinformatics/bow-tie/bowtie2-2.2.3/BT2_HOME:??

I can call up programs like pico using their full path like /usr/bin/pico.
Then a new window open
The header:GNU nano 2.0.6 New Buffer

The footer: ^G Get Help ^O WriteOut ^R Read File ^Y Prev Page ^K Cut Text ^C Cur Pos
^X Exit ^J Justify ^W Where Is ^V Next Page ^U UnCut Text^T To Spell

But these ^G/^O/^R/^Y.... anything is not working.

I guess the issue is that my PATH is messed up. How can I get back my path?

[GenoMax]

See if you are able to fix it with this: http://superuser.com/questions/60570...und-on-mac-osx Adjust additional values for PATH as needed.

[zillur]

Thank you very much. But how I open the vi editor to reset the path? as my my vi/vim command also not working.
Mds-MacBook-Pro:~ ZILLURRAHMAN$ vi
-bash: vi: command not found
Mds-MacBook-Pro:~ ZILLURRAHMAN$ vim
-bash: vim: command not found
Mds-MacBook-Pro:~ ZILLURRAHMAN$ -vi
-bash: -vi: command not found
Mds-MacBook-Pro:~ ZILLURRAHMAN$

[blancha]

Just type the full path to vi or vim.
It should be:
/usr/bin/vi
or
/usr/bin/vim

[GenoMax]

Thank you very much. But how I open the vi editor to reset the path? as my my vi/vim command also not working.
Mds-MacBook-Pro:~ ZILLURRAHMAN$ vi
-bash: vi: command not found
Mds-MacBook-Pro:~ ZILLURRAHMAN$ vim
-bash: vim: command not found
Mds-MacBook-Pro:~ ZILLURRAHMAN$ -vi
-bash: -vi: command not found
Mds-MacBook-Pro:~ ZILLURRAHMAN$

Use blancha's advice above or use a visual editor to make/edit the file (textedit). See: http://www.tech-recipes.com/rx/2618/...with_textedit/