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  • yuanzhi
    started a topic BEDTools - mergeBed -s option?

    BEDTools - mergeBed -s option?

    I am trying to use BEDTools - mergeBed to merge overlapping exons downloaded from UCSC. My goal is to find how many SNPs on the chr10 exons.

    I noticed that in the UCSC exon bed file

    chr10 82827 84054 NM_001164154_exon_0_0_chr10_82828_r 0 -
    chr10 84554 84665 NM_001164154_exon_1_0_chr10_84555_r 0 -
    chr10 84743 84852 NM_001164154_exon_2_0_chr10_84744_r 0 -
    chr10 85347 85504 NM_001164154_exon_3_0_chr10_85348_r 0 -
    chr10 170423 170832 NM_212479_exon_0_0_chr10_170424_f 0 +
    chr10 215933 216068 NM_212479_exon_1_0_chr10_215934_f 0 +
    chr10 245828 245988 NM_212479_exon_2_0_chr10_245829_f 0 +
    some exons are on the "-" strand, and some are on the "+" strand. I am wondering if I need use

    Code:
    mergeBed -s -i input.bed > output.bed
    to only merge exons that are on the same strand.

    This kind of strand issue has confused me for quite a long time...

    Thanks for all your help in advance

    -YZ

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