Closed zengfengbo closed 8 years ago
$ less WS-044-HGF_R1.fastq_1.gz|head -8 @NB501129:42:HJTWNBGXY:1:11101:3854:1054 1:N:0:AGATCG GTGCCNCACTTATACTGCAGCTGAGGGACCATGGAAAGCAGCCCACCCTGAGTTTTATACTCANGGGNGNNNNNNC + AAAAA#EEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE#EEE#A######E @NB501129:42:HJTWNBGXY:1:11101:7808:1055 1:N:0:AGATCG GGTGGNTGCCACTACTGCCTGGCTAATTTTTGTATTTTTATTAGAGATGGGGTTTCACCATGCNGGCNANNNNNNT + AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<#AEE#A######E
$ less WS-044-HGF_R1.fastq_1.gz|head -8|seqtk trimfq -b 0 - @NB501129:42:HJTWNBGXY:1:11101:3854:1054 1:N:0:AGATCG CACTTATACTGCAGCTGAGGGACCATGGAAAGCAGCCCACCCTGAGTTTTATACTCA + EEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE @NB501129:42:HJTWNBGXY:1:11101:7808:1055 1:N:0:AGATCG TGCCACTACTGCCTGGCTAATTTTTGTATTTTTATTAGAGATGGGGTTTCACCATGC + EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<
the tail Ns had trimed.
$ less WS-044-HGF_R1.fastq_1.gz|head -8|seqtk trimfq -b 0 -q 0.99 - @NB501129:42:HJTWNBGXY:1:11101:3854:1054 1:N:0:AGATCG GTGCCNCACTTATACTGCAGCTGAGGGACCATGGAAAGCAGCCCACCCTGAGTTTTATACTCANGGGNGNNNNNNC + AAAAA#EEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE#EEE#A######E @NB501129:42:HJTWNBGXY:1:11101:7808:1055 1:N:0:AGATCG GGTGGNTGCCACTACTGCCTGGCTAATTTTTGTATTTTTATTAGAGATGGGGTTTCACCATGCNGGCNANNNNNNT + AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<#AEE#A######E
normal, no base trimed.
$ less WS-044-HGF_R1.fastq_1.gz|head -8|seqtk trimfq -b 0 -q 0.09 - @NB501129:42:HJTWNBGXY:1:11101:3854:1054 1:N:0:AGATCG GTGCCNCACTTATACTGCAGCTGAGGGACCATGGAAAGCAGCCCACCCTGAGTTTTATACTCA + AAAAA#EEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE @NB501129:42:HJTWNBGXY:1:11101:7808:1055 1:N:0:AGATCG GGTGGNTGCCACTACTGCCTGGCTAATTTTTGTATTTTTATTAGAGATGGGGTTTCACCATGC + AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<
trim some base.
Options -b and -q don't work together. This is a limitation of trimfq. Sorry, no easy solutions.
-b
-q
given a fastq file.
I want trim 0bp from the fastq file.
the tail Ns had trimed.
add -q 0.99 option
normal, no base trimed.
add -q 0.09 option
trim some base.