Kallisto with paired-end bulk RNAseq with UMIs

mandino75 · 12-10-2018, 07:01 AM

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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12-10-2018, 07:01 AM	#1
mandino75 Junior Member Location: Spain Join Date: Dec 2018 Posts: 1	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