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jhangyu

join the data & gzip & run

Jun 8th, 2017
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  1. cat SRR391683_1.fastq SRR391700_1.fastq > eye_1.fastq
  2. cat SRR391683_3.fastq SRR391700_3.fastq > eye_3.fastq
  3.  
  4. cat SRR391681_1.fastq SRR391686_1.fastq SRR391696_1.fastq > heart_1.fastq
  5. cat SRR391681_3.fastq SRR391686_3.fastq SRR391696_3.fastq > heart_3.fastq
  6.  
  7. cat SRR391690_1.fastq SRR391695_1.fastq SRR391701_1.fastq > testis_1.fastq
  8. cat SRR391690_3.fastq SRR391695_3.fastq SRR391701_3.fastq > testis_3.fastq
  9.  
  10. cat SRR391697_1.fastq SRR391699_1.fastq > brain_1.fastq
  11. cat SRR391697_3.fastq SRR391699_3.fastq > brain_3.fastq
  12.  
  13. cat SRR391680_1.fastq SRR391684_1.fastq SRR391689_1.fastq > kidney_1.fastq
  14. cat SRR391680_3.fastq SRR391684_3.fastq SRR391689_3.fastq > kidney_3.fastq
  15.  
  16. cat SRR391688_1.fastq SRR391698_1.fastq > liver_1.fastq
  17. cat SRR391688_3.fastq SRR391698_3.fastq > liver_3.fastq
  18.  
  19. cat SRR391702_1.fastq SRR391704_1.fastq > muscle_1.fastq
  20. cat SRR391702_3.fastq SRR391704_3.fastq > muscle_3.fastq
  21.  
  22. cat SRR391682_1.fastq SRR391694_1.fastq > skin_1.fastq
  23. cat SRR391682_3.fastq SRR391694_3.fastq > skin_3.fastq
  24.  
  25. cat SRR391687_1.fastq SRR391691_1.fastq SRR391693_1.fastq > ovary_1.fastq
  26. cat SRR391687_3.fastq SRR391691_3.fastq SRR391693_3.fastq > ovary_3.fastq
  27.  
  28. for i in *.fastq ; do
  29.     pigz -k -p 24 $i
  30.     mv $i /mnt/2017_Tilapia_RNAseq
  31.     #gz ${i%%.*}.fastq
  32. done
  33.  
  34. 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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