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script_thursday
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#getting the data from SRA
wget --output-document sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
tar -vxzf sratoolkit.tar.gz
export PATH=$PATH:$PWD/sratoolkit.3.0.7-ubuntu64/bin
fastq-dump --stdout -X 2 SRR390728
fastq-dump --stdout -X 2 SRR390728
vdb-config -i
prefetch SRR8668759
fastq-dump --outdir fastq --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip ~/ncbi/public/sra/SRR2121685.sra
fastq-dump --outdir fastq --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip ~/home/ibg-4/course/SRAfetch/sra/SRR2121685.sra
fastq-dump --outdir fastq --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip SRAfetch/sra/SRR2121685.sra
ls fastq
java -jar ./Trimmomatic-0.39/trimmomatic-0.39.jar SE SRR17655907.fastq.gz SRR17655907.trim.fastq.gz
java -jar ./Trimmomatic-0.39/trimmomatic-0.39.jar SE course_data2/SRR17655898.fastq.gz course_data2/SRR17655898.trim.fastq.gz
SRR17655898.fastq.gz
java -jar ./Trimmomatic-0.39/trimmomatic-0.39.jar ourse_data2/SRR17655898.fastq.gz course_data2/SRR17655898.trim.fastq.gz I
LLUMINACLIP:./Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10
HEADCROP:5 SLIDINGWINDOW:4:15 MINLEN:70
java -jar Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 8 $input1 $input2 $output1 $output2 \
ILLUMINACLIP: Trimmomatic-0.39/adapters/TrueSeq3-PE-2.fa:2:30:10 \
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:70
java -jar Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 8 course_data2/SRR17655898.fastq.gz course_data2/SRR17655898.trimmed.fastq.gz \
ILLUMINACLIP:./Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 HEADCROP:5 \
SLIDINGWINDOW:4:15 MINLEN:70