Guillermo Carrasco guillermo-carrasco
guillermo-carrasco
/ simNGS_unique_ids.patch
Created
May 13, 2013 16:13
Unique read IDs for simLibrary
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| diff -ru simNGS.orig/src/simlibrary.c simNGS/src/simlibrary.c | |
| --- simNGS.orig/src/simlibrary.c 2013-05-13 17:45:17.000000000 +0200 | |
| +++ simNGS/src/simlibrary.c 2013-05-13 18:06:41.000000000 +0200 | |
| @@ -33,12 +33,13 @@ | |
| #define QUOTE(A) Q_(A) | |
| #define DEFAULT_COV 0.055 | |
| #define DEFAULT_OUT "fasta" | |
| +#define DEFAULT_UNIQUE "not" | |
| #define DEFAULT_INSERT 400 | |
| #define DEFAULT_NCYCLE 45 |
guillermo-carrasco
/ trim_data.sh
Last active
October 13, 2015 09:08
Small scrip to trim data for cancer/normal pipeline testing in AWS
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| #!/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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