memoll / miseq-test

miseq-test

Study through sequences

Unzip files

Gunzip $file.fastq.gz

View the size of the files

ls -lh

Count the number of fastq files in the folder

ls *.fastq | wc -l

Count the number of sequences in each file

grep "@M" -c *.fastq

Count primer sequences in each file

use . instead of wild-card nucleotides

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

Trim adapters

Trim using bbduk (in case adapters need to be trimmed)

If there are several fastq files

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

If there are only 2fastq files (R1 and R2)

/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