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  • #31
    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

    Comment


    • #32
      Thank you very much. Now I am learning some basic command lines.

      Comment


      • #33
        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

        Comment


        • #34
          Originally posted by zillur View Post
          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

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

          Comment


          • #35
            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

            Comment


            • #36
              Can you provide a long listing
              Code:
              $ ls -l
              of the directory? I thought your post above had the right file listed.

              Comment


              • #37
                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

                Comment


                • #38
                  Is that what you wanted?

                  Comment


                  • #39
                    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.

                    Code:
                    $ 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

                    Code:
                    $ 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

                    Comment


                    • #40
                      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

                      Comment


                      • #41
                        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

                        Comment


                        • #42
                          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$

                          Comment


                          • #43
                            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

                            Comment


                            • #44
                              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


                              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

                              Comment


                              • #45
                                Samtools needs to be compiled. Have you done a "make" in the samtools directory? Does not look like you have based on the listing.

                                Comment

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