Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bedtools sort by faidx

    The sort order of my bam file is:

    Code:
    cmccabe@DTV-A5211QLM:~/Desktop/NGS/pool_I_090215$ samtools view -H IonXpress_008_150902_newheader.bam | grep SQ | cut -f 2 | awk '{ sub(/^SN:/, ""); print;}'
    chr1
    chr2
    chr3
    chr4
    chr5
    chr6
    chr7
    chr8
    chr9
    chr10
    chr11
    chr12
    chr13
    chr14
    chr15
    chr16
    chr17
    chr18
    chr19
    chr20
    chr21
    chr22
    chrX
    chrY
    chrM
    So I created a names.txt to do a sortBed in bedtools but it appears that the option I need is not there.

    Code:
    Tool:    bedtools sort (aka sortBed)
    Version: v2.25.0
    Summary: Sorts a feature file in various and useful ways.
    
    Usage:   bedtools sort [OPTIONS] -i <bed/gff/vcf>
    
    Options: 
    	-sizeA			Sort by feature size in ascending order.
    	-sizeD			Sort by feature size in descending order.
    	-chrThenSizeA		Sort by chrom (asc), then feature size (asc).
    	-chrThenSizeD		Sort by chrom (asc), then feature size (desc).
    	-chrThenScoreA		Sort by chrom (asc), then score (asc).
    	-chrThenScoreD		Sort by chrom (asc), then score (desc).
    	-faidx (names.txt)	Sort according to the chromosomes declared in "names.txt"
    	-header	Print the header from the A file prior to results.
    
    cmccabe@DTV-A5211QLM:~/Desktop/NGS$ sortBed faidx -i /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets.bed > /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed
    
    *****ERROR: Unrecognized parameter: faidx *****
    Basically, since the sort order of my bam is in "human ordering" I wanted to sort my bed in the same way. Thank you .

  • #2
    Did you try

    Code:
    $ sortBed -faidx -i etc.

    Comment


    • #3
      I tried that and got:

      Code:
      Tool:    bedtools sort (aka sortBed)
      Version: v2.25.0
      Summary: Sorts a feature file in various and useful ways.
      
      Usage:   bedtools sort [OPTIONS] -i <bed/gff/vcf>
      
      Options: 
      	-sizeA			Sort by feature size in ascending order.
      	-sizeD			Sort by feature size in descending order.
      	-chrThenSizeA		Sort by chrom (asc), then feature size (asc).
      	-chrThenSizeD		Sort by chrom (asc), then feature size (desc).
      	-chrThenScoreA		Sort by chrom (asc), then score (asc).
      	-chrThenScoreD		Sort by chrom (asc), then score (desc).
      	-faidx (names.txt)	Sort according to the chromosomes declared in "names.txt"
      	-header	Print the header from the A file prior to results.
      
      
      cmccabe@DTV-A5211QLM:~/Desktop/NGS$ sortBed -faidx -i /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets.bed > /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed
      
      *****ERROR: Unrecognized parameter: /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets.bed *****
      I checked the directory where the bed is located as well:
      Code:
      cmccabe@DTV-A5211QLM:~/Desktop/NGS$ ls /home/cmccabe/Desktop/NGS/bed/bedtools
      names.txt  names.txt~  xgen_targets.bed  xgen_targets.bed~
      Thank you .

      Is there a better way to sort by human ordering for the bed file. I have searched but it appears "lexical" ordering is preferred. Thanks.
      Last edited by cmccabe; 09-28-2015, 12:30 PM.

      Comment


      • #4
        Did you actually read the output, or just copy and paste when it didn't work?

        Code:
        -faidx (names.txt)  Sort according to the chromosomes declared in "names.txt"
        You have to specify the sorting file when you issue the command, immediately after the option flag.

        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, 03-27-2024, 06:37 PM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-27-2024, 06:07 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        53 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