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guillermo-carrasco/trim_data.sh

Last active October 13, 2015 09:08
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Small scrip to trim data for cancer/normal pipeline testing in AWS
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trim_data.sh
#!/bin/bash
# Trim the data to the first 1.000.000 reads (4.000.000 lines)
zcat synthetic_challenge_set3_normal_NGv3_1.fq.gz | head -n 4000000 > synthetic_challenge_set3_normal_NGv3_1_trimmed.fq && gzip synthetic_challenge_set3_normal_NGv3_1_trimmed.fq
zcat synthetic_challenge_set3_normal_NGv3_2.fq.gz | head -n 4000000 > synthetic_challenge_set3_normal_NGv3_2_trimmed.fq && gzip synthetic_challenge_set3_normal_NGv3_2_trimmed.fq
zcat synthetic_challenge_set3_tumor_NGv3_1.fq.gz | head -n 4000000 > synthetic_challenge_set3_tumor_NGv3_1_trimmed.fq && gzip synthetic_challenge_set3_tumor_NGv3_1_trimmed.fq
zcat synthetic_challenge_set3_tumor_NGv3_2.fq.gz | head -n 4000000 > synthetic_challenge_set3_tumor_NGv3_2_trimmed.fq && gzip synthetic_challenge_set3_tumor_NGv3_2_trimmed.fq
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