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  • Kallisto with paired-end bulk RNAseq with UMIs

    Hi All,

    i have a paired-end bulk RNAseq generated with UMIs in order to reduce duplicates from PCR
    Since now, i used my own piepeline with STAR + UMI_tools to deal with the UMIs and generate a "clean duplicates " bam file, but I wnat to know if kallisto is able to deal with this data
    I have three fastq's : left and right paired-end FASTQs and one FASTQ for the UMIs.

    I used kallisto in pseudobam mode, first generating my batch file

    #id umi file1 file2
    sample UMI_001.fastq.gz B_L001_R1_001.fastq.gz B_R2_001.fastq.gz


    And then running kallisto in this way

    kallisto pseudo --index=/home/Genomes/Transcriptome_g1k_v37_kallisto_index -o kallisto_output -b batch.txt --umi -t 20 2>&1 | tee log.txt

    However, it seems that Kallisto with umi option is only capable to deal with single-end

    Am I right or maybe I forgot anything? Any ideas will be highly aprreciated


    Kind Regards

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