Question: Is Kallisto able to deal with UMIs and paired-end RNASeq?
gravatar for antgomo
23 months ago by
antgomo30 wrote:

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

rna-seq kallisto umi • 1.1k views
ADD COMMENTlink modified 23 months ago by genomax92k • written 23 months ago by antgomo30

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

-u  --umi          First file in pair is a UMI file
ADD REPLYlink modified 23 months ago • written 23 months ago by h.mon31k

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).

ADD REPLYlink written 23 months ago by antgomo30

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.

ADD REPLYlink written 23 months ago by h.mon31k
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