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- ./align_and_estimate_abundance.pl --transcripts /home/genomica/DATA/Lattuga/denovo_trinity_denovo_filtered_dump_completo/Trinity.fasta --seqType fq --single /home/genomica/DATA/Lattuga/DRR057309_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057310_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057311_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057312_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057313_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057314_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057315_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057316_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057317_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057318_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057319_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057320_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057321_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057322_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057323_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057324_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057325_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057326_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057327_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057328_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057329_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057330_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057331_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057332_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057333_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057059_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057060_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057061_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057062_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057063_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057064_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057065_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057066_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057067_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057068_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057069_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057070_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057071_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057072_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057073_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057074_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057075_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057076_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057077_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057078_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057079_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057080_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057081_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057082_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057083_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057084_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057085_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057086_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057087_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057088_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057089_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057090_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057091_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057092_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057093_1_clipped.fastq,/home/genomica/DATA/Lattuga/DRR057094_1_clipped.fastq --thread_count 60 --est_method RSEM --aln_method bowtie2 --trinity_mode --debug --output_dir /home/genomica/DATA/Lattuga/denovo_trinity_denovo_filtered_dump_completo/ --prep_reference --samples_file /home/genomica/DATA/Lattuga/denovo_trinity_denovo_filtered_dump_completo/Campioni
- export PATH=/home/genomica/DATA/Software/bowtie/bowtie2-2.3.3.1-linux-x86_64:$PATH
- Da eseguire da ./
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