Kallisto

jhangyu@jhangyuvm:/mnt/data/ncbi/Tilapia_Trinity_output$ kallisto index -i kallisto_index Trinity.fasta

[build] loading fasta file Trinity.fasta
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
        from 3395 target sequences
[build] counting k-mers ... done.
[build] building target de Bruijn graph ...  done
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 491161 contigs and contains 109907694 k-mers


kallisto quant -t 23 -i kallisto_index -o kallisto_out --pseudobam blood_1.fastq.gz blood_3.fastq.gz brain_1.fastq.gz brain_3.fastq.gz embryo_1.fastq.gz embryo_3.fastq.gz | samtools view -Sb - > out.bam
kallisto quant -i kallisto_index -o kallisto_out blood_1.fastq.gz blood_3.fastq.gz brain_1.fastq.gz brain_3.fastq.gz embryo_1.fastq.gz embryo_3.fastq.gz