Is Kallisto able to deal with UMIs and paired-end RNASeq?

Question

[antgomo]

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 output_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 appreciated

Thanks in advance

[h.mon]

When using kallisto pseudo --umi, kallisto considers the first file as UMIs:

-u  --umi          First file in pair is a UMI file

[antgomo]

Exactly, that's what I read. And is the the same that I put on batch.txt as you can see in my post, the point then (what i was asking) is if Kallisto is only able to deal with UMIs in single end mode (i.e first file UMI and second one FASTQ).

[h.mon]

kallisto bus can deal with several UMI schemes, but I don't know if it can deal with your particular case - I never used kallisto bus.