[GenoMax]

It appears that you must have downloaded the pre-compiled binary for OS X. In that case you do not need to "make"/compile the program. You should be able to run it directly (may need to add execute permissions to bowtie2 binary).

If you are new to command line/would like to pickup some basics of unix from this excellent resource: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

[zillur]

Thank you very much. Now I am learning some basic command lines.

[zillur]

Here is my files. When I started with the bowtie command terminal is showing the following result. What should I do now?
Mds-MacBook-Pro:~ ZILLURRAHMAN$ cd bowtie2-2.2.3
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ls
AUTHORS bowtie2-align-l-debug bowtie2-inspect-l
LICENSE bowtie2-align-s bowtie2-inspect-l-debug
MANUAL bowtie2-align-s-debug bowtie2-inspect-s
MANUAL.markdown bowtie2-build bowtie2-inspect-s-debug
NEWS bowtie2-build-l doc
TUTORIAL bowtie2-build-l-debug example
VERSION bowtie2-build-s scripts
bowtie2 bowtie2-build-s-debug
bowtie2-align-l bowtie2-inspect
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ./bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie: No such file or directory

[GenoMax]

bowtie2
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ./bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie: No such file or directory

The name of the program is bowtie2 so you should run

$ ./bowtie2 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT

[zillur]

Thank you very much. I have type the followings but.......

Mds-MacBook-Pro:~ ZILLURRAHMAN$ ./bowtie2 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie2: No such file or directory
Mds-MacBook-Pro:~ ZILLURRAHMAN$ ./bowtie2-2.2.3 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie2-2.2.3: is a directory
Mds-MacBook-Pro:~ ZILLURRAHMAN$ ./bowtie2 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie2: No such file or directory

[GenoMax]

Can you provide a long listing

$ ls -l

of the directory? I thought your post above had the right file listed.

[zillur]

Ya sure.

Mds-MacBook-Pro:~ ZILLURRAHMAN$ ls -l
total 4688
drwx------ 5 ZILLURRAHMAN staff 170 Sep 25 19:52 Applications
drwx------+ 9 ZILLURRAHMAN staff 306 Sep 19 15:21 Desktop
drwx------+ 12 ZILLURRAHMAN staff 408 Sep 22 15:00 Documents
drwx------+ 224 ZILLURRAHMAN staff 7616 Sep 25 19:25 Downloads
drwx------@ 50 ZILLURRAHMAN staff 1700 Sep 11 11:49 Library
drwx------+ 3 ZILLURRAHMAN staff 102 Aug 27 22:46 Movies
drwx------+ 7 ZILLURRAHMAN staff 238 Sep 3 18:11 Music
drwx------+ 5 ZILLURRAHMAN staff 170 Aug 28 09:57 Pictures
-rw-r--r--@ 1 ZILLURRAHMAN staff 2395395 Sep 3 14:53 PopulusHelp.pdf
drwxr-xr-x+ 6 ZILLURRAHMAN staff 204 Sep 25 19:57 Public
drwxr-xr-x@ 28 ZILLURRAHMAN staff 952 Sep 11 10:28 bowtie2-2.2.3
drwxr-xr-x 2 ZILLURRAHMAN staff 68 Sep 23 00:03 folder
drwxr-xr-x 2 ZILLURRAHMAN staff 68 Sep 23 00:03 new
drwxr-xr-x 3 ZILLURRAHMAN staff 102 Sep 23 00:05 newfolder
-rw-r--r-- 1 ZILLURRAHMAN staff 77 Aug 28 16:56 project.uprj

[zillur]

Is that what you wanted?

[GenoMax]

You are trying to run the program from the current folder which is the wrong folder (did you read about the concept of relative paths at the Korf UNIX site? This is an extremely important concept to learn, when you are new to command line).

Based on your file listing try (from the directory where you provided the long list)

I do not remember if the e_coli data comes with the program. If it is there in the bowtie2 folder then you can omit (/you_need_to_provide_path_to/) part.

$ bowtie2-2.2.3/bin/bowtie2 -a -v 2 /you_need_to_provide_path_to/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT

or

$ cd bowtie2-2.2.3
$ bin/bowtie2 -a -v 2 /you_need_to_provide_path_to/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT

[zillur]

Thank you very much. Now my bowtie2 is working. Can you give me some beginner tips to build an index. I have this:

mds-macbook-pro:bow-tie ZILLURRAHMAN$ cd bowtie2-2.2.3
mds-macbook-pro:bowtie2-2.2.3 ZILLURRAHMAN$ ls
AUTHORS bowtie2-align-l-debug bowtie2-inspect-l
LICENSE bowtie2-align-s bowtie2-inspect-l-debug
MANUAL bowtie2-align-s-debug bowtie2-inspect-s
MANUAL.markdown bowtie2-build bowtie2-inspect-s-debug
NEWS bowtie2-build-l doc
TUTORIAL bowtie2-build-l-debug example
VERSION bowtie2-build-s scripts
bowtie2 bowtie2-build-s-debug
bowtie2-align-l bowtie2-inspect
mds-macbook-pro:bowtie2-2.2.3 ZILLURRAHMAN$ cd example
mds-macbook-pro:example ZILLURRAHMAN$ ls
index reads reference
mds-macbook-pro:example ZILLURRAHMAN$ cd index
mds-macbook-pro:index ZILLURRAHMAN$ ls
lambda_virus.1.bt2 lambda_virus.3.bt2 lambda_virus.rev.1.bt2
lambda_virus.2.bt2 lambda_virus.4.bt2 lambda_virus.rev.2.bt2

[GenoMax]

In this case the index is already pre-built for lambda virus (the files in the index directory).

I would suggest getting prebuilt sequence/index/annotation bundle from Illumina iGenomes site if you are working with a genome available there: http://support.illumina.com/sequenci...e/igenome.html. Otherwise you can follow the directions here to build a bowtie2 index: http://bowtie-bio.sourceforge.net/bo...-build-indexer

[zillur]

Thank you very much. Now can you tell me in which point I am wrong?
Here is my files and commands.


Mds-MacBook-Pro:~ ZILLURRAHMAN$ cd desktop/bioinformatics
Mds-MacBook-Pro:bioinformatics ZILLURRAHMAN$ cd bow-tie
Mds-MacBook-Pro:bow-tie ZILLURRAHMAN$ cd bowtie2-2.2.3
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ls
AUTHORS bowtie2-align-l-debug bowtie2-inspect
LICENSE bowtie2-align-s bowtie2-inspect-l
MANUAL bowtie2-align-s-debug bowtie2-inspect-l-debug
MANUAL.markdown bowtie2-build bowtie2-inspect-s
NEWS bowtie2-build-l bowtie2-inspect-s-debug
TUTORIAL bowtie2-build-l-debug doc
VERSION bowtie2-build-s example
bowtie2 bowtie2-build-s-debug scripts
bowtie2-align-l bowtie2-buildc
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ cd example
Mds-MacBook-Pro:example ZILLURRAHMAN$ ls
commands index reads reference
Mds-MacBook-Pro:example ZILLURRAHMAN$ cd index
Mds-MacBook-Pro:index ZILLURRAHMAN$ ls
lambda_virus.1.bt2 lambda_virus.4.bt2 lambdaout
lambda_virus.2.bt2 lambda_virus.rev.1.bt2
lambda_virus.3.bt2 lambda_virus.rev.2.bt2
Mds-MacBook-Pro:index ZILLURRAHMAN$ cd ..
Mds-MacBook-Pro:example ZILLURRAHMAN$ cd reads
Mds-MacBook-Pro:reads ZILLURRAHMAN$ ls
longreads.fq reads_1.fq reads_2.fq simulate.pl
Mds-MacBook-Pro:reads ZILLURRAHMAN$ cd ..
Mds-MacBook-Pro:example ZILLURRAHMAN$ cd reference/
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
lambda_virus.fa lambdaout.4.bt2 out
lambdaout.1.bt2 lambdaout.rev.1.bt2 out.sam
lambdaout.2.bt2 lambdaout.rev.2.bt2
lambdaout.3.bt2 nohup.out
Mds-MacBook-Pro:reference ZILLURRAHMAN$ cd ..
Mds-MacBook-Pro:example ZILLURRAHMAN$ open commands
Mds-MacBook-Pro:example ZILLURRAHMAN$ nohup bowtie2 -x lambdaout -q ../reads/reads_1.fq, ../reads/reads_2.fq -S out.sam
appending output to nohup.out
Mds-MacBook-Pro:example ZILLURRAHMAN$ tail nohup.out
Extra parameter(s) specified: "../reads/reads_2.fq"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/Bioinformatics/Bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x lambdaout -q -S out.sam ../reads/reads_1.fq, ../reads/reads_2.fq
(ERR): bowtie2-align exited with value 1
Mds-MacBook-Pro:example ZILLURRAHMAN$ ls
commands index nohup.out reads reference
Mds-MacBook-Pro:example ZILLURRAHMAN$

[GenoMax]

What other contents are there in nohup.out file?

Are you following the steps in the bowtie tutorial here: http://bowtie-bio.sourceforge.net/bo...-phage-example

[zillur]

Thank you very much. Now after making the paths for indexing, build, align I can align bowtie2 files. 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. I have downloaded samtools from

http://sourceforge.net/projects/samtools/files/latest/download?source=files

Now do I need to make path for the executables using such command lines
(export SAMTOOLS_HOME=/Users/ecerami/libraries/samtools-0.1.19
export PATH=$SAMTOOLS_HOME:$PATH
export PATH=$SAMTOOLS_HOME/bcftools/:$PATH
export PATH=$SAMTOOLS_HOME/misc/:$PATH)

There are too many files. Which are executables? If all are executables do I need to make path for all of these?

Regards
Zillur

Here is my files.
AUTHORS
bam_aux.c
bam_cat.c
bam_color.c
bam_endian.h
bam_flags.c
bam_import.c
bam_index.c
bam_lpileup.c
bam_lpileup.h
bam_mate.c
bam_md.c
bam_plbuf.c
bam_plbuf.h
bam_plcmd.c
bam_reheader.c
bam_rmdup.c
bam_rmdupse.c
bam_sort.c
bam_split.c
bam_stat.c
bam_tview_curses.c
bam_tview_html.c
bam_tview.c
bam_tview.h
bam.c
bam.h
bam2bcf_indel.c
bam2bcf.c
bam2bcf.h
bam2depth.c
bamshuf.c
bamtk.c
bedcov.c
bedidx.c
ChangeLog.old
cut_target.c
errmod.c
errmod.h
examples
faidx.c
htslib-1.1
INSTALL
kaln.c
kaln.h
kprobaln.c
kprobaln.h
LICENSE
Makefile
Makefile.mingw
misc
NEWS
padding.c
phase.c
README
sam_header.c
sam_header.h
sam_view.c
sam.c
sam.h
sample.c
sample.h
samtools.1
samtools.h
stats_isize.c
stats_isize.h
stats.c

[GenoMax]

Samtools needs to be compiled. Have you done a "make" in the samtools directory? Does not look like you have based on the listing.