Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How can I extract each APAsite possibility from this table?

    Hello,

    I have an output from APATrap package, which gives back the predicted APA sites from samples. I need to make a list from all the possibles APAs to cross it with miRNAs database and get known if there is a match. The problem is a have a huges lists from 16 samples, and I need a way to automatize this task for reproducibility.

    I have this summed up table:

    Predicted_APA.TOTAL Loci.TOTAL

    41867799,41867388,41866990 chr17:41866927-41867904

    And I need something like this:

    CHR Loci.UTR.TOTAL Locus initial Locus Final

    chr17 41866927-41867799 41866927 41867799
    chr17 41866927-41867388 41866927 41867388
    chr17 41866927-41866990 41866927 41866990

    Do you know any tip or clue to do it for 16 samples with 1000 results each one?

    Thanks in advance, and sorry if my question isn't appropriate. I will answer any question for further people in the same situation.
    Beginner @ RNA-Seq, R programming, Linux, Python.-

    Please be patients!

  • #2
    I got this answer from another forum, so I add it here in case someone needs it.

    input:
    $cat test.txt

    Predicted_APA.TOTAL Loci.TOTAL
    41867799,41867388,41866990 chr17:41866927-41867904
    output:
    $awk -v FS='[-:\t]' -v OFS="\t" ' NR != 1 {split($1,a,","); for (i in a) {print $2,$3"-"a[i],$3,a[i]}}' test.txt

    chr17 41866927-41867799 41866927 41867799
    chr17 41866927-41867388 41866927 41867388
    chr17 41866927-41866990 41866927 41866990
    Beginner @ RNA-Seq, R programming, Linux, Python.-

    Please be patients!

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM
    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-28-2024, 06:12 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    77 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X