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- cat SRR391683_1.fastq SRR391700_1.fastq > eye_1.fastq
- cat SRR391683_3.fastq SRR391700_3.fastq > eye_3.fastq
- cat SRR391681_1.fastq SRR391686_1.fastq SRR391696_1.fastq > heart_1.fastq
- cat SRR391681_3.fastq SRR391686_3.fastq SRR391696_3.fastq > heart_3.fastq
- cat SRR391690_1.fastq SRR391695_1.fastq SRR391701_1.fastq > testis_1.fastq
- cat SRR391690_3.fastq SRR391695_3.fastq SRR391701_3.fastq > testis_3.fastq
- cat SRR391697_1.fastq SRR391699_1.fastq > brain_1.fastq
- cat SRR391697_3.fastq SRR391699_3.fastq > brain_3.fastq
- cat SRR391680_1.fastq SRR391684_1.fastq SRR391689_1.fastq > kidney_1.fastq
- cat SRR391680_3.fastq SRR391684_3.fastq SRR391689_3.fastq > kidney_3.fastq
- cat SRR391688_1.fastq SRR391698_1.fastq > liver_1.fastq
- cat SRR391688_3.fastq SRR391698_3.fastq > liver_3.fastq
- cat SRR391702_1.fastq SRR391704_1.fastq > muscle_1.fastq
- cat SRR391702_3.fastq SRR391704_3.fastq > muscle_3.fastq
- cat SRR391682_1.fastq SRR391694_1.fastq > skin_1.fastq
- cat SRR391682_3.fastq SRR391694_3.fastq > skin_3.fastq
- cat SRR391687_1.fastq SRR391691_1.fastq SRR391693_1.fastq > ovary_1.fastq
- cat SRR391687_3.fastq SRR391691_3.fastq SRR391693_3.fastq > ovary_3.fastq
- for i in *.fastq ; do
- pigz -k -p 24 $i
- mv $i /mnt/2017_Tilapia_RNAseq
- #gz ${i%%.*}.fastq
- done
- Trinity --trimmomatic --seqType fq --max_memory 63G --output '/mnt/data/ncbi/Tilapia_Trinity_output' --left blood_1.fastq.gz,brain_1.fastq.gz,embryo_1.fastq.gz --right blood_3.fastq.gz,brain_3.fastq.gz,embryo_3.fastq.gz --CPU 23 > Trinity_log.out
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