Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Intersecting multiple bed files

    Hello,

    I have several RNA-Seq transcript data sets assembled and in BED format. I have masked out previously identified transcripts from the data, leaving me with "unidentified" transcripts. A visual of this data in the UCSC Genome Browser is attached.

    I need to computationally gather the locations where all of the resulting transcripts intersect. In looking though the bedtools intersect function, it seems that there is no option to specify regions where ALL the files intersect, only those where at least 2 of the supplied files intersect.

    Have any of you encountered this issue before? What are your suggested workarounds? Would I need to continually compare 2 files and then keep comparing that output to the next file and so on? Or is there an option I am unaware of/another software function that can handle this?

    Thank you all very much!
    -Anna
    Attached Files

  • #2
    bedops --intersect first.bed second.bed third.bed > result.bed

    Comment


    • #3
      Perfect, thanks!

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      50 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