Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • ENCODE ChIP-seq Metrics (NSC,RSC)

    Hello all,

    I was wondering if there's a software package that calculates the metrics that are used by ENCODE project (described in http://genome.cshlp.org/content/22/9/1813 )

    I'm interested in NSC, RSC and data for "cross-correlation - strand shift" plots.

    Anybody else uses those for their experiments?

    Thank you in advance.

  • #2
    SPP package

    Hi,

    download and in install the spp R-package from here



    This package has a function 'get.binding.characteristics' which will do the job.

    Peter

    Comment


    • #3
      Awesome, thank you for the advice!

      Comment


      • #4
        Hello,

        I would use this script



        It uses SPP as well. It's convenient.

        Comment


        • #5
          Originally posted by mthornton View Post
          Dear All,

          I am a newbie in ChIP-seq analysis and now I am trying to assess these values using "phantompeakqualtools", but unfortunately I got an error and cant find any similar posts for that.
          Would you please help me !

          I used this command to determine strand cross-correlation peak:

          Rscript /data/NGS/phantompeakqualtools/run_spp.R -c=ChIP-WT1-R2-BWA_sorted_unique.bam -savp -out=R2unique-phantom

          and I got the following error:

          awk: line 2: function and never defined
          Error converting BAM to tagalign file: /tmp/RtmpbkYntW/ChIP-WT1-R2-BWA_sorted_unique.bam6f036a95b6e

          I assumed that the error was due to the input file and tried the following command to first convert BAM to tagalign

          samtools view -F 0x0204 -o - ChIP-WT1-R1_sorted_unique.bam | awk 'BEGIN{OFS="\t"}{if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c > ChIP-WT1-R1_sorted_unique.tagAlign.gz

          and again I got the following error;
          awk: line 2: function and never define

          So, now I know that the problem is due to awk. But I can't understand what it is exactly!

          I would be happy to hear your comments.

          Thanks in advance.

          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
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X