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  • the usage of convert2bed

    Hi,

    Anyone has used the convert2bed?

    I got confusing about how to use it. My input file is 1.sam, output file is 1.bed.


    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

    Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF
    and WIG genomic formats to BED or BEDOPS Starch (compressed BED)

  • #2
    The --input (or -i) argument is the format, not the actual input file. It expects input on stdin, which you can pass by using the "<" operator.

    Comment


    • #3
      As the Usage is trying to tell you... You need to add the following flags to your command:
      --input=bam --output=bed
      Also, convert2bed reads/writes through stdin and stdout, which in your case means:
      < 1.sam > 1.bed

      Comment


      • #4
        Thanks, sarvidsson and yueluo.

        I got the right answer.

        convert2bed -i SAM < 1.sam > 1.bed

        Comment


        • #5
          I also include convenience wrapper scripts with BEDOPS, so that you can do:

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

          Similar wrapper scripts are available for other formats supported by convert2bed (BAM, GFF, GVF, PSL, WIG, etc.).

          Comment

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