Could you please tell me how can I work with fastq file to generate counts matrix data as .txt file for R studio?

10 October 2016 1 9K Report

I have fastq data from Illumina next generation sequencing. I would like to work with this data in R studio to generate heatmap. To generate heat map R studio needs counts matrix data as .txt file. Could you please tell me how can I work with fastq file to generate matrix data as .txt file for R studio?

Thanks in advance.....

Manvendra Singh

You could just run RSEM using STAR

http://deweylab.github.io/RSEM/

it would give you level of expression in FPKM, TPM and counts,

you can immediately import it in R and play around

hth

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