Hello,
I am very new to bioinformatics stuff. I have a bed file and I want to filter sequences which starts with GGG. I used grep but it gave all sequences that have GGG.
This is example file:
chr1 3165857 3165877 GGGGGGGTCGCCTTTAATAC_494 559.876 +
chr1 3172959 3172979 ACGAGGGGGGTCATCTTTTT_1280 166.748 -
chr1 3176088 3176108 ATCGAGGGGGTGATGTTTTT_2924 29.7413 +
chr1 3207150 3207170 CCGGGGGAATCGACTTTGGA_265 795.823 -
chr1 3207151 3207171 ACCGGGGGAATCGACTTTGG_186 884.041 -
chr1 3207154 3207174 CCGACCGGGGGAATCGACTT_182 888.415 -
chr1 3220405 3220425 TTGGGTGGGGGGCAGAGTCT_273 786.893 +
Is there any way to define in grep (or anything else) to search in the beginning of the string?
Thanks,
Alan
I am very new to bioinformatics stuff. I have a bed file and I want to filter sequences which starts with GGG. I used grep but it gave all sequences that have GGG.
This is example file:
chr1 3165857 3165877 GGGGGGGTCGCCTTTAATAC_494 559.876 +
chr1 3172959 3172979 ACGAGGGGGGTCATCTTTTT_1280 166.748 -
chr1 3176088 3176108 ATCGAGGGGGTGATGTTTTT_2924 29.7413 +
chr1 3207150 3207170 CCGGGGGAATCGACTTTGGA_265 795.823 -
chr1 3207151 3207171 ACCGGGGGAATCGACTTTGG_186 884.041 -
chr1 3207154 3207174 CCGACCGGGGGAATCGACTT_182 888.415 -
chr1 3220405 3220425 TTGGGTGGGGGGCAGAGTCT_273 786.893 +
Is there any way to define in grep (or anything else) to search in the beginning of the string?
Thanks,
Alan
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