Entering edit mode
4.5 years ago
charadriussp
•
0
Hello all,
Could you tell me how to trim adapters using flexbar during RNA seq data processing, if I have many files, please?
I am beginner and I study the course in GriffithLab (Introduction to bioinformatics for RNA sequence analysis). It's input files are:
HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz
UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz
UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz
UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz
UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz
UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz
The decision in course (how to trim adapters) is (https://rnabio.org/module-02-alignment/0002/02/01/Adapter_Trim/):
flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT --adapters $RNA_REFS_DIR/illumina_multiplex.fa --pre-trim-left 13 --max-uncalled 300 --min-read-length 25 --threads 8 --zip-output GZ --reads $RNA_DATA_DIR/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz --reads2 $RNA_DATA_DIR/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz --target $RNA_DATA_TRIM_DIR/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22
flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT --adapters $RNA_REFS_DIR/illumina_multiplex.fa --pre-trim-left 13 --max-uncalled 300 --min-read-length 25 --threads 8 --zip-output GZ --reads $RNA_DATA_DIR/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz --reads2 $RNA_DATA_DIR/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz --target $RNA_DATA_TRIM_DIR/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22
flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT --adapters $RNA_REFS_DIR/illumina_multiplex.fa --pre-trim-left 13 --max-uncalled 300 --min-read-length 25 --threads 8 --zip-output GZ --reads $RNA_DATA_DIR/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz --reads2 $RNA_DATA_DIR/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz --target $RNA_DATA_TRIM_DIR/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22
flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT --adapters $RNA_REFS_DIR/illumina_multiplex.fa --pre-trim-left 13 --max-uncalled 300 --min-read-length 25 --threads 8 --zip-output GZ --reads $RNA_DATA_DIR/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz --reads2 $RNA_DATA_DIR/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz --target $RNA_DATA_TRIM_DIR/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22
flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT --adapters $RNA_REFS_DIR/illumina_multiplex.fa --pre-trim-left 13 --max-uncalled 300 --min-read-length 25 --threads 8 --zip-output GZ --reads $RNA_DATA_DIR/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz --reads2 $RNA_DATA_DIR/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz --target $RNA_DATA_TRIM_DIR/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22
flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT --adapters $RNA_REFS_DIR/illumina_multiplex.fa --pre-trim-left 13 --max-uncalled 300 --min-read-length 25 --threads 8 --zip-output GZ --reads $RNA_DATA_DIR/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz --reads2 $RNA_DATA_DIR/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz --target $RNA_DATA_TRIM_DIR/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22
I think it is very long for more than this number of files. I tried to replace the different symbols by *, but had the error: flexbar: Too many arguments!
Thank you in advance!
What you need is a bash
for
loop, see these posts:bash loop for alignment RNA-seq data
Bash Script Loop Help
Bash Script Loop Help
cutadapt loop and paired-end reads