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  • *.bed file

    Hi,

    How I can produce the *.bed file?

    I have two file: one is genome.fa and the other is RNA-seq.fa. Following is the RNA-seq.fa format.

    Anyone can recommend the appropriate software to produce the *.bed file?

    Thanks a lot!

    Li

    >t0000001_x537124
    CCCGACCTCAGATCAGATGA
    >t0000002_x340107
    TCACCGGGTAGACATTCATTAT
    >t0000003_x268409
    TGAAAGACATGGGTAGTGAGAT
    >t0000004_x172657
    CGATATGTGGTAATTTGGATGA
    >t0000005_x154782
    AGAGGTAGTGATTCAAAAAGTT
    >t0000006_x140076
    TCACCGGGTAGACATTCATTATA
    >t0000007_x131590
    TGAGATCACTATGAAAGCTGG
    >t0000008_x125368
    TGAGGTAGAATGTTGGATGACT
    >t0000009_x120455
    TGAGTATTGCATCAAGAACCGA
    >t0000010_x95804
    TCCCTGAGACCATTGACTGCAT
    >t0000011_x78210
    TGGACGGAAGTGTAATGAGGGT
    >t0000012_x73438
    TGAGGTAGATTGTTGGATGACT
    >t0000013_x68884
    CCCGACCTCAGATCAGATG
    >t0000014_x60358
    TGAAAGACACAGGTAGTGGGACA
    >t0000015_x59786
    TGGAATGTCGAGAAATATGCAT
    >t0000016_x44935
    TCCCTGAGACCATTGACT
    >t0000017_x40270
    TCACCGGGTAGACATTCATTCT
    >t0000018_x38439
    AGATATGTTTGGTTAATTGGTGA
    >t0000019_x38425
    TGAGATCACTATGAAAGCTGGT

  • #2
    1. Align the reads to the genome. Bowtie would be a likely candidate.
    2. Use bam2bed from bedops to convert the BAM file to BED format.


    You might need to use samtools to convert from SAM to BAM, as I haven't a clue if bam2bed accepts SAM format. You can probably pipe all of this together too.

    Comment


    • #3
      It is unusual to see fasta format raw data (if that is indeed original data).

      Do the sequence ID's have any specific meaning (>t0000016_x44935)?

      Comment


      • #4
        Hi, dpryan,

        You are right!

        I tried bedops to convert SAM to BED. How to use the convert2bed? I tried mant times, but it seems doesn't work.


        Thanks a lot!

        li



        li@li-Lenovo:~$ convert2bed -i 1.sam > 1.bed
        convert2bed
        version: 2.4.12
        author: Alex Reynolds

        Usage:

        $ convert2bed --input=fmt [--output=fmt] [options] < input > output

        Comment


        • #5
          Try
          Code:
          convert2bed -i SAM < 1.sam > 1.bed

          Comment


          • #6
            Thanks sarvidsson,

            You are right!

            Comment


            • #7
              As noted in another question, convenience wrapper scripts are provided to convert SAM and other formats to BED and Starch (compressed BED):

              $ sam2bed < 1.sam > 1.bed
              $ sam2starch < 1.sam > 1.starch

              These are included with default BEDOPS installations.

              Comment

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