Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    No I currently do not, to save time. I will try it with the GEM file though. I'll let you know how it goes!

    Comment


    • #17
      Oh I forgot to ask about the circos format script. I plugged in my *ratios.txt file and got some output. But it does not look like circos format to me, how am I supposed to use the output given from this script?

      Comment


      • #18
        If it looks like:

        Code:
        hs1 1631000 1731000 3.953692
        hs1 1731000 1831000 3.953692
        hs1 1831000 1931000 3.953692
        hs1 1931000 2031000 3.953692
        Circos will undestand it. You should add to the Circos config something like:

        Code:
        <plot>
        show    = yes
        type    = scatter
        file = yourFile.CNP.circos.txt
        
        glyph = rectangle
         glyph_size = 4
         fill_color = dgrey
         stroke_color = dgrey
         stroke_thickness = 1
        
        min   = 0
        max   = 6
        #r0    = 0.7r
        #r1    = 0.975r
        r0    = 0.76r
        r1    = 0.975r
        
        background       = no
        background_color = vvlgrey
        background_stroke_color = black
        background_stroke_thickness = 1
        
        axis           = yes
        axis_color     = lgrey
        axis_thickness = 1
        axis_spacing   = 1
        
        <rules>
        
        <rule>
        importance   = 100
        condition    = var(value) >= 6
        value=6
        glyph = rectangle
         glyph_size = 4
         fill_color = red
         stroke_color = red
         stroke_thickness = 1
        </rule>
        
        <rule>
        importance   = 100
        condition    = var(value) > 2.5 && var(value) < 6
        glyph = rectangle
         glyph_size = 4
         fill_color = orange
         stroke_color = orange
         stroke_thickness = 1
        </rule>
        
        <rule>
        importance   = 85
        condition    = var(value) < 1.5
         glyph_size = 4
         fill_color = blue
         stroke_color = blue
         stroke_thickness = 1
        </rule>
        
        <rule>
        show=0
        importance   = 85
        condition    = var(value) < 0
        color = blue
        </rule>
        </rules>
        
        </plot>
        Last edited by valeu; 07-30-2014, 07:00 AM.

        Comment


        • #19
          Calling CNA and BAF for exome seq data without a control

          Hi, I'm trying to use FREEC to call CNA and BAF in some exome seq samples, but haven't been able to make it work. The tool ran fine on the chr19 test data.

          The problems I'm seeing are
          - the tool runs but doesn't generate any of the output files except mpileup.txt_sample.cpn
          It exits with the error message:
          ..There is no control sample!!!
          You have to use a matching control sample to get adequite results since GC-bias is not the only bias in targeted sequencing

          - even the .cpn file doesn't seem right because it tries to call copy number outside the target regions I provided via the TruSeq_exome_targeted_regions.hg19.bed
          and not surprisingly calls them all as 0 copy number.


          I'm running the tool on a pileup generated using samtools v.0.1.12. I'm using the following config file:


          [general]
          chrLenFile=hg19.len

          window = 3000
          step = 1000
          ploidy = 2

          #breakPointThreshold = -.001

          #GCcontentProfile = GC_profile.cnp

          intercept=1
          minMappabilityPerWindow = 0.7

          outputDir = .

          sex=XY
          breakPointType=4

          #degree=3
          #coefficientOfVariation = 0.05
          #gemMappabilityFile = /hg19/out76_hg19.gem

          chrFiles = FREEC_Linux64/chromosomes/

          [sample]

          mateFile=mpileup.txt
          #mateCopyNumberFile=mpileup.txt_sample.cpn

          inputFormat = pileup
          mateOrientation = FR

          [control]

          [BAF]

          SNPfile = hg19_snp131.SingleDiNucl.1based.txt
          minimalCoveragePerPosition = 5


          [target]
          captureRegions=TruSeq_exome_targeted_regions.hg19.bed

          Comment


          • #20
            Hi, at this moment there is no option to run FREEC on exome-seq data without control sample. But since you are the second person who wants to do it, I will probably add this option soon.

            Comment


            • #21
              That would really useful!
              My backup was to use per-exon mean target coverage generated by Picard HS Metrics, with some added correction for %GC, but I'd rather use your tool.
              Thanks,
              -Ben

              Comment


              • #22
                Display of CNV-data in IGV

                Hi, I am struggling with displaying CNV data generated with freec in IGV. Can somebody give me some advice how to display CNVs in an inutitive way?

                Thanks!

                Comment


                • #23
                  Hi!

                  I think I should right a script to create a .WIG file from _ratio.txt (http://www.broadinstitute.org/igv/WIG)

                  If you code in perl, you could do it yourself and share the script. Otherwise, I will do it when I have time

                  Comment


                  • #24
                    Thanks for your reply! It would be very helpful if you could implement a script for .WIG file creation!
                    :-)

                    Comment


                    • #25
                      Version 5.7 of Control-FREEC can now create BedGraph tracks on demand. Just set

                      Code:
                      [general]
                      BedGraphOutput=TRUE
                      This format is supported by the UCSC genome browser as well as IGV (http://www.broadinstitute.org/software/igv/bedgraph)

                      Comment


                      • #26
                        Hi

                        I am (slowly) trying to integrate Control-FREEC into a pipeline, and I was wondering if there's a way to generate a GC-content profile outside of running the whole thing once. Like maybe one of the already existing scripts could be called outside of freec first?

                        Comment


                        • #27
                          Hi,

                          I have not foreseen an option to create a GC-content profile outside of FREEC. But you could make a trick: something like providing a read file with 10 reads and setting a window size.

                          I will think about adding a separate function to calculate this profile.

                          Comment


                          • #28
                            Hi,

                            so now you can generate a GC-content profile independently from FREEC:
                            http://bioinfo-out.curie.fr/projects...orial.html#GCP

                            Comment


                            • #29
                              a unusual problem in FREEC

                              I meet an unusual problem when I run FREEC. If I provide a mateCopyNumberFile, and then qsub, it will run sucessfully, but in fact I normally don't have mateCopyNumberFile, but if I don't provide it, it can't run, the error message is:

                              sh:samtools:command not found

                              Error: FREEC was not able to extract reads from /database/chenxi/task/cancerProgram/pipline/bwa/BPMICS4/sortedbam/PD1W_XXL_BPMICS4_NoIndex_modified.bam

                              Check your parameters: inputFormat and matesOrientation
                              Use "matesOrientation=0" if you have single end reads
                              Check the list of possible input formats at http://bioinfo-out.curie.fr/projects...al.html#CONFIG



                              I can't figure out what happens here. My parameters are absolutely correct, and I have samtools in my working directory and environmental PATH.

                              Can anyone give me some helps? I am not able to run FREEC because of this.

                              Comment


                              • #30
                                I think I know what happens. When you provide mateCopyNumberFile, FREEC does not try to read your .BAM file. When there is no mateCopyNumberFile available FREEC tries to read your file by calling "samtools" in the command line. And it seems that "samtools" does not point to anything.

                                I would suggest two solutions:
                                1. in the bash script that you qsub, add something like
                                  Code:
                                  export PATH=$PATH:/pathToSamtools
                                  #check whether samtools exists
                                  samtools 2>samtools.usage.txt
                                  #run FREEC
                                  freec -conf myCofig.txt
                                1. transform you .BAM file to .SAM. Then, FREEC will not need samtools.


                                If you prefer, you can write to me directly to [email protected]

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Strategies for Sequencing Challenging Samples
                                  by seqadmin


                                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                  03-22-2024, 06:39 AM
                                • 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

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, Yesterday, 06:37 PM
                                0 responses
                                8 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, Yesterday, 06:07 PM
                                0 responses
                                8 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-22-2024, 10:03 AM
                                0 responses
                                49 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-21-2024, 07:32 AM
                                0 responses
                                67 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X