Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #31
    I'm really at a loss as to what's going on. Could you cd into the "/cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0" directory, type "ls -l", take a screen shot, and attach it?

    Comment


    • #32
      Also for fun do "head -3 Amplicons.bed | od -c" and "head -3 hg19_genome.txt | od -c" and copy and paste the output here.

      Comment


      • #33
        I concur. Everything looks ok and should work. Let us see what the output is for the commands Heisman asked for.

        Comment


        • #34
          bed2Bam

          The results of the 3 commands:
          cmccabe@DTV-L2231M5J ~
          $ cd "/cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0"

          cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
          $ ls -l
          total 177
          -rwx------+ 1 cmccabe Domain Users 43671 Jul 10 13:27 Amplicons.bed
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 bin
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 data
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 docs
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 genomes
          -rwx------+ 1 cmccabe Domain Users 484 Jul 10 09:40 hg19_genome.txt
          -rwx------+ 1 cmccabe Domain Users 17988 Nov 3 2012 LICENSE
          -rwx------+ 1 cmccabe Domain Users 6693 Nov 3 2012 Makefile
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 obj
          -rwx------+ 1 cmccabe Domain Users 1505 Nov 3 2012 README.rst
          -rwx------+ 1 cmccabe Domain Users 32293 Nov 3 2012 RELEASE_HISTORY
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 scripts
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 src
          drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 test

          cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
          $ head -3 Amplicons.bed | od -c
          0000000 c h r 1 \t 2 1 6 0 2 9 0 \t 2 1 6
          0000020 0 4 7 5 \t S K I \t . \t A M P L 2
          0000040 6 8 8 8 2 8 3 5 2 \n c h r 1 \t 2
          0000060 1 6 0 4 8 0 \t 2 1 6 0 6 3 4 \t S
          0000100 K I \t . \t A M P L 2 6 8 8 8 2 9
          0000120 5 3 0 \n c h r 1 \t 2 1 6 0 6 3 2
          0000140 \t 2 1 6 0 7 3 8 \t S K I \t . \t A
          0000160 M P L 2 6 8 8 8 2 8 0 5 8 \n
          0000176

          cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
          $ head -3 hg19_genome.txt | od -c
          0000000 c h r 1 \t 2 4 9 , 2 5 0 , 6 2 1
          0000020 \t \t \n c h r 2 \t 2 4 3 , 1 9 9 ,
          0000040 3 7 3 \t \t \t \n c h r 3 \t 1 9 8 ,
          0000060 0 2 2 , 4 3 0 \t \t \t \n
          0000073
          Thank you.

          Comment


          • #35
            Originally posted by cmccabe View Post
            I re-compiled in cygwin

            did dos2unix Amplicons.bed
            dos2unix hg19_genome.txt

            both of those files are tab- deliminated

            and the commands I used in Cygwin:

            $ cd "/cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0"

            $ bin/bamToBed -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam

            Amplicons.bed (went from 44kb to 43kb)
            chr1 2160290 2160475 SKI . AMPL2688828352
            chr1 2160480 2160634 SKI . AMPL2688829530
            chr1 2160632 2160738 SKI . AMPL2688828058

            hg19_genome.txt (1kb) - acc chromosomes and lenghths are in this file
            chr1 249,250,621
            chr2 243,199,373

            Amplicons.bam is still 0kb and not working.
            I just read through this thread and while I don't have anything to offer I did notice that the command call was switched around again in this post (bamToBed instead of bedToBam).
            /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
            Salk Institute for Biological Studies, La Jolla, CA, USA */

            Comment


            • #36
              Looks like you have some extra tabs in the hg19_genome.txt file.

              Can you try the genomes file supplied by bedtools in "genomes\human.hg19.genome"?

              Code:
              $ bin/bamToBed -i Amplicons.bed -g genomes/human.hg19.genome > Amplicons.bam

              Comment


              • #37
                bed2bam

                cmccabe@DTV-L2231M5J ~
                $ cd "C:\Users\cmccabe\Desktop\Ion_Torrent_ Software\bedtools-2.17.0"

                cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
                $ bin/bedToBam -i Amplicons.bed -g genomes/human.hg19.genome > Amplicons.bam

                The resulting BAM file is 0kb

                Amplicons.bed: (~43kb after dos2unix)
                chr1 2160290 2160475 SKI . AMPL2688828352
                chr1 2160480 2160634 SKI . AMPL2688829530
                chr1 2160632 2160738 SKI . AMPL2688828058

                Thanks.

                Comment


                • #38
                  I am fresh out of ideas as to what to do next.

                  Do you have a colleague who has access to a Mac/unix machine? Perhaps it would be best to try this conversion there.

                  Comment


                  • #39
                    Maybe the first lines of your Amplicons.bed are ok but later lines aren't? Could you try "head -2 Amplicons.bed > Amplicons_3lines.bed" and then run it with the new file?

                    Also try to run the command without the "> Amplicons.bam" part and see if you get any output directly to the screen.

                    If that doesn't work, try to run "mergeBed" instead of "bedToBam" like this: "bin/mergeBed -i Amplicons.bed" and see if something outputs to the screen, just to make sure there isn't something specifically weird with the "bedToBam" program.

                    Comment


                    • #40
                      I'm with GenoMax though; really wish I could teleport to your computer to try to figure this out.

                      Comment


                      • #41
                        bed2bam

                        I am in the process of using ubuntu 12.0.4 and at the point of compiling the binaries. I have the gcc compilier but what is the command for the zlib and python. I think those where the 3 things needed. Thanks.

                        Comment


                        • #42
                          Start making sure that you have the compilation essentials installed (make, gcc etc)

                          Code:
                          sudo apt-get install build-essential
                          and then get the rest

                          Code:
                          sudo apt-get install zlib zlib-devel python

                          Comment


                          • #43
                            bed2Bam

                            When I use the code below I get unable to locate zlib-devel
                            Code:
                            sudo apt-get install zlib zlib-devel python
                            Thank you very much.

                            Comment


                            • #44
                              Try this instead of the previous zlib:

                              Code:
                              sudo apt-get install zlib1g zlib1g-dev

                              Comment


                              • #45
                                Bed2Bam

                                Bedtools 2.17 is compilied on Ubuntu and the command:

                                bin/bamToBed -i Amplicons.bed -g genomes/human.hg19.genome > Amplicons.bam does run but there is an error extracting the gz file and it is 0 bytes. Thanks.

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Exploring Human Diversity Through Large-Scale Omics
                                  by seqadmin


                                  In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                                  Today, 06:43 AM
                                • seqadmin
                                  Best Practices for Single-Cell Sequencing Analysis
                                  by seqadmin



                                  While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
                                  06-06-2024, 07:15 AM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 06-21-2024, 07:49 AM
                                0 responses
                                224 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 06-20-2024, 07:23 AM
                                0 responses
                                230 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 06-17-2024, 06:54 AM
                                0 responses
                                231 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 06-14-2024, 07:24 AM
                                0 responses
                                28 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X