procedure to build a Kallisto index for the genome hg19+ERCC+18S/28S
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,
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sahar.taheri91 •
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sahar.taheri91 •
1 answer
- 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
READMEfile to understand the difference between the two downloads.
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