Gunzip $file.fastq.gz
ls -lh
ls *.fastq | wc -l
grep "@M" -c *.fastq
grep "$primer_sequence" -c *.fastq
- F-primer 799F (R1): AACMGGATTAGATACCCKG
grep "AAC.GGATTAGATACCC.G" -c *.fastq
- R-primer 1115R (R2): AGGGTTGCGCTCGTTG
grep "AGGGTTGCGCTCGTTG" -c *.fastq
for i in *.fastq; do /data/apps/bbmap/bbduk.sh in=$i out=adapter-trimmed/$i-trimmed.fastq ref=/data/apps/bbmap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1 tbo tpe; done
/data/apps/bbmap/bbduk.sh -Xmx1g in=file_R#_001.fastq out=adapter-trimmed/file-trimmed_R#.fastq ref=/data/apps/bbmap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1 tbo tpe