Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Wig File Formats

    Hello,
    I am having problems regarding wig files. I wanted to know the names/accession numbers of genes having certain histone modifications. Most papers are genome wide having chip-on-chip information and they give the supplementary information in wig files. I am unable to interpret the files. Need help regarding this issue .....

  • #2
    please see UCSC website: http://www.genome.ucsc.edu/goldenPath/help/wiggle.html

    Comment


    • #3
      Thanks for the link. I have pasted the first few entries in the wig file and this is how it looks. I viewed it in the UCSC genome browser. I am confused regarding the cut off I should be taking...do I have to consider the regions having 1 or 2 as entries...
      Kindly reply...

      track type=wiggle_0 name="GMAT_H3K9K14ac2" description="GMAT_H3K9K14ac2_hg18" visibility=full autoScale=off viewLimits=0.0:15.0 color=0,0,0

      variableStep chrom=chr1 span=21

      554973 1

      554990 3

      556480 1

      559247 2

      559431 2
      .........etc
      Last edited by Sanchari; 05-10-2010, 10:08 PM.

      Comment


      • #4
        What do you see in UCSC browser that you are not expecting?
        SpliceMap: De novo detection of splice junctions from RNA-seq
        Download SpliceMap Comment here

        Comment


        • #5
          UCSC will show the peaks for histone modifications for sure....but I wanted to know the specific list of genes whose promoters are having those modifications.....my wig file contains a huge number of chromosomal locations and I wanted to know which of these are coinciding with gene promoters....

          Comment


          • #6
            Sorry, I'm not too familiar with the display of histone modifications, so I can't help you there.

            But, I'm guessing you are looking for a way to find gene annotations which are close to significant peaks automatically?
            SpliceMap: De novo detection of splice junctions from RNA-seq
            Download SpliceMap Comment here

            Comment


            • #7
              Yea...ur right..I need the gene names having significant peaks...

              Comment


              • #8
                Originally posted by Sanchari View Post
                Yea...ur right..I need the gene names having significant peaks...

                hmm... I'm not aware of an automatic way of doing that. However, it is possible to download the annotations as a text file. Maybe you can write a short script to search through them based on the location of the peaks in the wig file.
                SpliceMap: De novo detection of splice junctions from RNA-seq
                Download SpliceMap Comment here

                Comment


                • #9
                  yea...ok....I'll have to write some scripts to map the annotation data to the wig file..

                  Comment

                  Latest Articles

                  Collapse

                  • seqadmin
                    Latest Developments in Precision Medicine
                    by seqadmin



                    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

                    Somatic Genomics
                    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
                    05-24-2024, 01:16 PM
                  • seqadmin
                    Recent Advances in Sequencing Analysis Tools
                    by seqadmin


                    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
                    05-06-2024, 07:48 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, 05-24-2024, 07:15 AM
                  0 responses
                  13 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 05-23-2024, 10:28 AM
                  0 responses
                  17 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 05-23-2024, 07:35 AM
                  0 responses
                  20 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 05-22-2024, 02:06 PM
                  0 responses
                  10 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X