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  • #16
    Originally posted by cdinz View Post
    I have the same question too. It would be really great if someone can shed some light on it.
    The input type will not vary, it will still be a BAM file aligned to the ref genome.
    The difference comes in the analysis part.
    You will have to take into consideration the Intron-Exon Junctions. As a Intron will be taken as a CNV. Also another problem is that if a CNV breakpiomt lies in the Intron, you can not come to know about it.
    We have tumor Exome data, done by the True-Seq protocol, hence while doing the analysis use the co-ordinates provided by them.

    Comment


    • #17
      Originally posted by mimi_lupton View Post
      Dear all,
      I have a couple of questions regarding CNV-seq.
      I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

      "Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

      I think this is some kind of Perl script error??

      Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

      Thanks for you help
      Hello mimi,

      I am trying to work on custom capture data usin cnv-seq. Could you enlighten me on how it worked for you and any suggestions on how to use it would be greatly appreciated.

      Thanks,
      Praful

      Comment


      • #18
        CNV-seq ref.hits file?

        Hello

        I am analyzing CNVs for the first time or rather new to CNV-seq. Manual is pretty clear but i have one very basic doubt. I have my .bam file for which i can generate my.hits file as well using samtools. BUT from where do i get this ref.hits file. I have only one .bam file thats it which i would be using for my.hits file.. Some guidance?

        Comment


        • #19
          Originally posted by parveendabas View Post
          Hello

          I am analyzing CNVs for the first time or rather new to CNV-seq. Manual is pretty clear but i have one very basic doubt. I have my .bam file for which i can generate my.hits file as well using samtools. BUT from where do i get this ref.hits file. I have only one .bam file thats it which i would be using for my.hits file.. Some guidance?
          Hi Parveen,
          The ref.hits would be from a normal/control sample... or if you don't have one... You can get the normal bam file from the 1000 Genomes project.

          -Dinesh
          Last edited by DineshCyanam; 11-24-2011, 03:47 AM.

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          • #20
            Thank you dinesh. But my data is not normal/control type and neither its related to 1000 genome project. Its one sample data. What should i do??

            Comment


            • #21
              Originally posted by parveendabas View Post
              Thank you dinesh. But my data is not normal/control type and neither its related to 1000 genome project. Its one sample data. What should i do??
              Well you still need to compare it with against a normal. See post #9 above.
              https://www.seqanswers.com/node/138425

              or

              try CNVnator from Mark Gerstein's lab. You don't need to supply a ref file for CNVnator. More info and link to papers here: http://sv.gersteinlab.org/

              Comment


              • #22
                Hello!
                Does the CNV-seq be used in genome (sequenced by Illumina -Short reads) in haploids apicomplexa?
                Any thoughs?
                Thanks a lot.
                difereg

                Comment


                • #23
                  Originally posted by mimi_lupton View Post
                  Dear all,
                  I have a couple of questions regarding CNV-seq.
                  I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

                  "Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

                  I think this is some kind of Perl script error??

                  Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

                  Thanks for you help
                  Ever get an answer for this 'value as an ARRAY reference" problem? i'm having the same issue..

                  Comment


                  • #24
                    help

                    I'm running the CNV-seq package and I keep getting the following error:

                    write read-counts into file: test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.count
                    R package cnv output: test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv
                    Error in library(cnv) : there is no package called 'cnv'
                    Execution halted

                    Can someone please help me out?

                    Btw, the data I'm using is the sample data available on the CNV-seq website.

                    Thank you

                    Comment


                    • #25
                      Can't use an undefined value as an ARRAY reference

                      While running CNV-seq, sometimes it works perfectly but sometimes i end with the following error "Can't use an undefined value as an ARRAY reference at line 205, <REF> line 1119928258".
                      The same has been asked many a times but no solution yet. Anyone to help out or some other suggestion for alternate CNV detection algorithms?

                      Comment


                      • #26
                        @adurasiwam3:
                        It indicates, you dont have the CNV R package installed into correct place (or at all).

                        Assuming your machine has R.
                        you install the package by issuing following command while inside the package's root folder.

                        R CMD INSTALL /cnv/

                        If your syestem's R is not in the path, you need to call it explicitly (eg. /apps/bin/R) instead of R.

                        Hope this helps.

                        Comment


                        • #27
                          it helped!

                          thank you ragowthaman

                          Comment


                          • #28
                            can someone explain how the sensitivity/specificity for CNV-seq is calculated in the CNV-seq paper?

                            Where can I get data with simulated CNVs (including the known positions)?

                            Thank you!

                            Comment


                            • #29
                              Hi CNV-seq users. I am having a bit of trouble understanding how the cnv caller works.

                              The results of one of my .cnv files is as follows:


                              "22" 16275937 18988591 204 2822 17632264 -0.683143010100174 2.46090424342812e-08 0 NA NA NA
                              "22" 17632265 20344919 195 3190 18988592 -0.925076474377026 2.85143491959854e-12 0 NA NA NA
                              "22" 18988593 21701247 191 3107 20344920 -0.916943777560497 3.8950753868117e-12 0 NA NA NA
                              "22" 20344921 23057575 188 3082 21701248 -0.928128374311553 2.53633054795169e-12 0 NA NA NA
                              "22" 21701249 24413903 210 3108 23057576 -0.780591350215992 6.85565176334874e-10 0 NA NA NA
                              "22" 23057577 25770231 206 3256 24413904 -0.875450536557434 1.90371570869566e-11 0 NA NA NA
                              "22" 24413905 27126559 177 3139 25770232 -1.04154984297352 3.22421238629005e-14 0 NA NA NA
                              "22" 25770233 28482887 180 3103 27126560 -1.00066096467345 1.55775796481263e-13 0 NA NA NA
                              "22" 27126561 29839215 157 2718 28482888 -1.00677507135017 1.23086398489238e-13 0 NA NA NA
                              "22" 28482889 31195543 143 2606 29839216 -1.08081611126415 7.11362307806884e-15 0 NA NA NA
                              "22" 29839217 32551871 160 2852 31195544 -1.04889625103093 2.42971963892229e-14 0 NA NA NA
                              "22" 31195545 33908199 155 2827 32551872 -1.08199784203134 6.7976211176428e-15 0 NA NA NA
                              "22" 32551873 35264527 166 2610 33908200 -0.867860739584727 2.5422391389699e-11 0 NA NA NA
                              "22" 33908201 36620855 170 2621 35264528 -0.839576781665121 7.44538364328285e-11 0 NA NA NA
                              "22" 35264529 37977183 210 3210 36620856 -0.827178143817948 1.19029886619997e-10 0 NA NA NA
                              "22" 36620857 39333511 218 3208 37977184 -0.772340181152399 9.32704407763649e-10 0 NA NA NA
                              "22" 37977185 40689839 195 2891 39333512 -0.783088659201844 6.24484354174541e-10 0 NA NA NA
                              "22" 39333513 42046167 191 2608 40689840 -0.664365405669734 4.82741849789952e-08 0 NA NA NA
                              "22" 40689841 43402495 306 4365 42046168 -0.727444175298556 4.90998416767461e-09 0 NA NA NA
                              "22" 42046169 44758823 409 5386 43402496 -0.612107561034328 3.04270126227705e-07 0 NA NA NA
                              "22" 43402497 46115151 273 3718 44758824 -0.660619993474034 5.51777958936528e-08 0 NA NA NA
                              "22" 44758825 47471479 193 3190 46115152 -0.939949750858556 1.61095440200424e-12 0 NA NA NA

                              Surely this should have been annotated as a cnv as there are more than 4 windows with a log2<-0.6 and high significance !
                              Moreover I find the coordinates strange:
                              look at the first and third line:
                              "22" 16275937 18988591
                              "22" 18988593 21701247

                              18988591 is not equal to 18988593. Whereas sometimes, if I change the window size the end of the first line and the beginning of the third would be the same.

                              These files were created with default values, window size = 2712655

                              Thanks in advance for any insight you can give me. I am tempted to call the cnvs manually...what would be the best way to do so from the .cnv file ?

                              Comment


                              • #30
                                Hi!
                                I've got a chromosome with 3 deletions and woudl like to have them all in the same plot, but it seems I can only choose 1 CNV at a time:
                                >plot.cnv(data, CNV=2, upstream=2e+6, downstream=2e+6)

                                Any suggesion?

                                Comment

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