Kallisto quantification

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2.8 years ago

shubhamvermauoh • 0

I'm doing de novo transcriptomics where no genome and transcriptome is available.

In the study, I've used three time points i.e., control(0 hour stress), 3 hour stress and 6 hour stress treatment.

For the RNA quantification, I'm using Kallisto tool for which I need to generate an index file. Which fastq data or file I should use for the generation of index which I can used for the quantification purpose.

Thank you in advance

kallisto RNA-Seq • 909 views

ADD COMMENT • link updated 2.7 years ago by Ram 43k • written 2.8 years ago by shubhamvermauoh • 0

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kallisto will need an index of the transcriptome of the organism. You can download premade index files from this link if your organism is on that list. Otherwise you will need to create one.

ADD REPLY • link 2.8 years ago by GenoMax 141k

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Thank you for your response. My organism is completely new and it's not listed over there. Can you please tell me how to create the index

ADD REPLY • link 2.8 years ago by shubhamvermauoh • 0

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You use a transcriptome in fasta format to build the index, please see the kallisto manual. Does your organism has any kind of reference transcriptome? If not you will need to assemble one from RNA-seq data.

ADD REPLY • link 2.7 years ago by ATpoint 82k

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