Question

procedure to build a Kallisto index for the genome hg19+ERCC+18S/28S

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6.2 years ago

sahar.taheri91 • 0

Dear all Hi,

I am a CS student with no background in biology. For the dataset GSE65683 I want to download genome to build Kallisto transcriptome index. The point is that I do not know how to do it for this hg19+ERCC+18S/28S genome. Actually, which source is good to download a reference genome and then for the +ERCC+18S/28S part what should I do to get the Kallisto index.

Thanks,

genome alignment rna-seq • 2.7k views

ADD COMMENT • link updated 6.2 years ago by GenoMax 154k • written 6.2 years ago by sahar.taheri91 • 0

score 3 · Answer 1 · 2019-08-25

Get protein coding transcript sequences for hg19 genome build from GENCODE (see below).
ERCC spike-in sequences from Thermo (bundle also contains annotation, you only need sequence)
Human 18S rRNA sequence from ENA/EBI
Human 28S rRNA sequence from ENA/EBI

cat these sequence files together and then proceed to build kallisto index.

Alternatively cDNA/CDS sequences can also be downloaded from Ensembl's hg19 site. Look at the README file to understand the difference between the two downloads.