Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • normalizing multicov output

    Hi..

    i used multicov to get read counts for specific genomic regions from different samples. Now, i would like to get expression values for those samples by normalizing the data. Can anyone suggest how i can proceed in doing that. i am attaching the sample output below

    HTML Code:
    Chromosome Name	Start	End	Strand	Sample 1	Sample 2	Sample 3	Sample 4	Sample 5	Sample 6
    Gm01	75	93	+	0	0	0	0	0	0
    Gm01	142	433	+	0	0	0	0	0	0
    Gm01	42335623	42335702	+	631	84	42	76	98	112
    Gm01	27758807	27763057	+	557	149	123	306	550	645
    Gm01	50818678	50819255	+	529	264	120	11	102	64
    Gm01	27753335	27757417	+	308	85	72	148	242	264

  • #2
    Why do not you use TopHat?

    Comment


    • #3
      Hi.. i have around million genome coordinates and i am not sure whether tophat can handle that many data points. Also, the genome coordinates vary from 20bp to 10kb regions.

      Comment


      • #4
        It is depends on the computational resources. It is worth to make a try.

        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