Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Can or should we perform feature counting with `bedtools intersect -c`?

    I have the following BAM file and a annotation file.
    What I want to do is to calculate reads count in
    I can do it with the following three methods.


    Below is the code

    Code:
        #!/bin/bash
        INPUT_BAM=my_paired_end_alignment.bam
        ANNNOT_BED=peak_annot.bed
        ANNNOT_GTF=peak_annot.gtf
        
        # Temporary file
        ALIGNMENT_BED=my_paired_end_alignment.bed
        
        #-----------
        # Method 1
        #-----------
        FINAL_COUNT_METHOD1=output_method1.txt
        bedtools bamtobed -bedpe -i $INPUT_BAM > $ALIGNMENT_BED
        bedtools intersect -a $ANNOT_BED -b $ALIGNMENT_BED -c > $FINAL_COUNT_METHOD1
        
        #-----------
        # Method 2
        #-----------
        FINAL_COUNT_METHOD2=output_method2.txt
        bedtools multicov -bams $INPUT_BAM -bed $ANNOT_BED > $FINAL_COUNT_METHOD2
        
        #-----------
        # Method 3
        #-----------
        featureCounts  -a $ANNOT_GTF -o counts.txt $INPUT_BAM
    The result given by Method1 is so different from Method2 (totally uncorrelated),
    whereas Method2 is highly correlated with Method3.

    My question is Method1 the right way to count feature? If not why?
    Should we use Method2 or Method3 instead?

  • #2
    For reference cross-posted: https://www.biostars.org/p/270366/

    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
    49 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