Originally posted by GenoMax
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Originally posted by SES
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after filtering from the command :
## quality filter
fastq_quality_filter -i SRR1561197_1.fastq -q 28 -p 100 -Q33 -o SRR1561197_1_filt.fastq
fastq_quality_filter -i SRR1561197_2.fastq -q 28 -p 100 -Q33 -o SRR1561197_2_filt.fastq
then i did trimming:
fastx_trimmer -i SRR1561197_1_filt.fastq -l 100 -f 14 -o SRR1561197_1_filt_trim.fastq
fastx_trimmer -i SRR1561197_2_filt.fastq -l 100 -f 14 -o SRR1561197_2_filt_trim.fastq
## add pair info to reads and remove comment to reduce size
pairfq addinfo -i SRR1561197_1_filt_trim.fastq -o SRR1561197_1_filt_trim_info.fastq -p 1
pairfq addinfo -i SRR1561197_1_filt_trim.fastq -o SRR1561197_2_filt_trim_info.fastq -p 2
## pair the reads
time pairfq makepairs -f SRR1561197_1_filt_trim_info.fastq \
-r SRR1561197_2_filt_trim_info.fastq \
-fp SRR1561197_1__p.fastq \
-rp SRR1561197_2__p.fastq \
-fs SRR1561197_1_s.fastq \
-rs SRR1561197_2_s.fastq \
--stats
Still i get all reads in these two files:
-fs SRR1561197_1_s.fastq \
-rs SRR1561197_2_s.fastq \
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