2021 sewon labnote

Jingpung resequencing - trimmomatic result

java -jar /data/Program/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 jinpung_1.fastq.gz jinpung_2.fastq.gz output_forward_paired.fastq.gz output_forward_unpaired.fastq.gz output_reverse_paired.fastq.gz output_reverse_unpaired.fastq.gz ILLUMINACLIP:/data/Program/Trimmomatic-0.39/adapters/TruSeq3-PE.fa :2:30:10 SLIDINGWINDOW:4:20 MINLEN:36

TrimmomaticPE: Started with arguments:

-phred33 jinpung_1.fastq.gz jinpung_2.fastq.gz output_forward_paired.fastq.gz output_forward_unpaired.fastq.gz output_reverse_paired.fastq.gz output_reverse_unpaired.fastq.gz ILLUMINACLIP:/data/Program/Trimmomatic-0.39/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36

Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences ll Input Read Pairs: 42918512 Both Surviving: 40100414 (93.43%) Forward Only Surviving: 2273317 (5.30%) Reverse Only Surviving: 297601 (0.69%) Dropped: 247180 (0.58%) TrimmomaticPE: Completed successfully

Jingpung making .bam file (w/ 20threads & q 30)

bwa mem -t 20 /data/ref/Gmax/assembly/Gmax_275_v2.0.fa ./jinpung_forward_paired.fastq.gz ./jingpung_reverse_paired.fastq.gz | samtools view -bS -q 30 -> jinpung.bam