Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • error with htseq count and bed tool

    hello every one,

    as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
    1. I am using Bedtool to count read in as
    Code:
    bedtools multicov -bams sample1.bam sample2.bam sample3.bam -bed all.gff3
    here in spite of bed file i am using reference genome file all.gff3. is it correct to use it ?
    Because I am not sure that I will get proper result with these gff3 file or not
    2. I am getting error with ht-seq as it is already installed in my machine but still it is showing that

    Code:
    [root@localhost ~]# htseq-count
    bash: htseq-count: command not found...
    Kindly reply me

    Thanks
    Last edited by meghavarshney; 07-01-2015, 09:16 PM. Reason: error

  • #2
    1) It may be installed, but it's not in your path. Look at where it was installed and either change your $PATH variable or use the full path to specify the executable.
    2) You shouldn't be running things like this as root.

    Comment


    • #3
      I had installed it in this location and still m not able to access it
      Code:
      [root@localhost HTSeq-0.6.1]# python setup.py install --user
      running install
      running bdist_egg
      running egg_info
      writing HTSeq.egg-info/PKG-INFO
      writing top-level names to HTSeq.egg-info/top_level.txt
      writing dependency_links to HTSeq.egg-info/dependency_links.txt
      reading manifest file 'HTSeq.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      no previously-included directories found matching 'example_data'
      no previously-included directories found matching 'test'
      warning: no previously-included files found matching 'todo.txt'
      writing manifest file 'HTSeq.egg-info/SOURCES.txt'
      installing library code to build/bdist.linux-x86_64/egg
      running install_lib
      running build_py
      running build_ext
      creating build/bdist.linux-x86_64/egg
      creating build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/__init__.py -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/_HTSeq_internal.py -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/StepVector.py -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/_version.py -> build/bdist.linux-x86_64/egg/HTSeq
      creating build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/scripts/__init__.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/scripts/qa.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/scripts/count.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/_HTSeq.so -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/_StepVector.so -> build/bdist.linux-x86_64/egg/HTSeq
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/__init__.py to __init__.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_HTSeq_internal.py to _HTSeq_internal.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/StepVector.py to StepVector.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_version.py to _version.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/__init__.py to __init__.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/qa.py to qa.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/count.py to count.pyc
      creating stub loader for HTSeq/_HTSeq.so
      creating stub loader for HTSeq/_StepVector.so
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_HTSeq.py to _HTSeq.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_StepVector.py to _StepVector.pyc
      creating build/bdist.linux-x86_64/egg/EGG-INFO
      installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      running install_scripts
      running build_scripts
      creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      copying build/scripts-2.7/htseq-qa -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      copying build/scripts-2.7/htseq-count -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/htseq-qa to 755
      changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/htseq-count to 755
      copying HTSeq.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
      copying HTSeq.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
      copying HTSeq.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
      copying HTSeq.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
      writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
      zip_safe flag not set; analyzing archive contents...
      HTSeq.StepVector: module references __file__
      creating 'dist/HTSeq-0.6.1-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
      removing 'build/bdist.linux-x86_64/egg' (and everything under it)
      Processing HTSeq-0.6.1-py2.7-linux-x86_64.egg
      removing '/root/.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg' (and everything under it)
      creating /root/.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg
      Extracting HTSeq-0.6.1-py2.7-linux-x86_64.egg to /root/.local/lib/python2.7/site-packages
      Removing HTSeq 0.6.1p1 from easy-install.pth file
      Adding HTSeq 0.6.1 to easy-install.pth file
      Installing htseq-qa script to /root/.local/bin
      Installing htseq-count script to /root/.local/bin
      
      Installed /root/.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg
      Processing dependencies for HTSeq==0.6.1
      Finished processing dependencies for HTSeq==0.6.1
      as i had tried it in these ways
      Code:
      [pinky@localhost HTSeq-0.6.1]$ htseq-count
      bash: htseq-count: command not found...
      [pinky@localhost HTSeq-0.6.1]$ python htseq-count
      python: can't open file 'htseq-count': [Errno 2] No such file or directory
      [pinky@localhost HTSeq-0.6.1]$ python /home/pinky/Downloads/HTSeq-0.6.1/htseq-count
      python: can't open file '/home/pinky/Downloads/HTSeq-0.6.1/htseq-count': [Errno 2] No such file or directory
      but still the problem remains same.

      Comment


      • #4
        Normally python programs end up in ~/.local/bin when you install them like this. Have a look there and add that to your path.

        Comment


        • #5
          i had checked but still i didn't find
          Code:
          [pinky@localhost bin]$ htseq-count
          bash: htseq-count: command not found...
          as from root this folder contain
          Code:
          [root@localhost bin]# ls
          annotateBed                                  getOverlap
          bam2bed                                      gff2bed
          bam2bed_gnuParallel                          gff2starch
          bam2bed_sge                                  groupBy
          bam2starch                                   gtf2bed
          bam2starch_gnuParallel                       gtf2starch
          bam2starch_sge                               gvf2bed
          bamToBed                                     gvf2starch
          bamToFastq                                   intersectBed
          bed12ToBed6                                  linksBed
          bedextract                                   mapBed
          bedmap                                       maskFastaFromBed
          bedops                                       mergeBed
          bedpeToBam                                   multiBamCov
          bedToBam                                     multiIntersectBed
          bedToIgv                                     nucBed
          bedtools                                     pairToBed
          closestBed                                   pairToPair
          closest-features                             psl2bed
          clusterBed                                   psl2starch
          complementBed                                R
          convert2bed                                  randomBed
          coverageBed                                  rmsk2bed
          expandCols                                   rmsk2starch
          fasta_clipping_histogram.pl                  Rscript
          fasta_formatter                              sam2bed
          fastaFromBed                                 sam2starch
          fasta_nucleotide_changer                     shuffleBed
          fastq_masker                                 slopBed
          fastq_quality_boxplot_graph.sh               sort-bed
          fastq_quality_converter                      sortBed
          fastq_quality_filter                         starch
          fastq_quality_trimmer                        starchcat
          fastq_to_fasta                               starchcluster_gnuParallel
          fastx_artifacts_filter                       starchcluster_sge
          fastx_barcode_splitter.pl                    subtractBed
          fastx_clipper                                tagBam
          fastx_collapser                              trimmomatic-0.30.jar
          fastx_nucleotide_distribution_graph.sh       unionBedGraphs
          fastx_nucleotide_distribution_line_graph.sh  unstarch
          fastx_quality_stats                          vcf2bed
          fastx_renamer                                vcf2starch
          fastx_reverse_complement                     wig2bed
          fastx_trimmer                                wig2starch
          fastx_uncollapser                            windowBed
          flankBed                                     windowMaker
          genomeCoverageBed
          [root@localhost bin]#
          so is their any other way to tackle this problem.

          Comment


          • #6
            That looks like ~/bin, not ~/.local/bin. The installation log you posted even showed that that's where it put the executables.

            Comment


            • #7
              Originally posted by meghavarshney View Post
              I had installed it in this location and still m not able to access it
              Code:
              [root@localhost HTSeq-0.6.1]# python setup.py install --user
              ...
              Installing htseq-qa script to /root/.local/bin
              Installing htseq-count script to /root/.local/bin
              I think you have done something weird here: You have installed the packages as root using the option --user. This installed htseq-count in the root home directory,/root/.local/bin. As regular user you can't access /root/.local/bin as it's not on path.

              If you execute python setup.py install --user as regular user you should be fine and see htseq-count in ~/.local/bin/.

              Comment


              • #8
                thnkxx

                thnkx to both of you . i got solution as for this i reinstalled HTSeq again as a regular user and now its properly working for me .


                thankx again

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM
                • seqadmin
                  The Impact of AI in Genomic Medicine
                  by seqadmin



                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                  02-26-2024, 02:07 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 03-14-2024, 06:13 AM
                0 responses
                34 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-08-2024, 08:03 AM
                0 responses
                72 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-07-2024, 08:13 AM
                0 responses
                82 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-06-2024, 09:51 AM
                0 responses
                68 views
                0 likes
                Last Post seqadmin  
                Working...
                X