Question: get gene ids running sleuth kallisto for differential gene expression
0
gravatar for frida.danielsson
4.5 years ago by
European Union
frida.danielsson40 wrote:

Hi,

I'm trying to run sleuth to look for differential gene expression between two conditions, but I find the manual a bit hard to interpret.

After running kallisto I have extensions in the transcript IDs (like "ENST00000632859.1") and I assume that's why I cannot get the output data mapped to gene IDs while running biomaRt as described in the "getting started" webpage, anyone knows how to deal with this? Can I just remove the extensions in the .tsv file or do I need to change something in the bootstrap file as well?

rna-seq kallisto sleuth • 2.6k views
ADD COMMENTlink modified 4 months ago by jocelyn.petitto10 • written 4.5 years ago by frida.danielsson40

Did you use their transcriptome index? Because that one gives me nicely formatted name, causing no problem to map them to the gene names.

ADD REPLYlink written 4.5 years ago by WouterDeCoster44k

I used a fasta file for the human genome looking like this:

>ENST00000448914.1 havana_ig_gene:known chromosome:GRCh38:14:22449113:22449125:1 gene:ENSG00000228985.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene
ACTGGGGGATACG...

Maybe I should try rebuild my index and rerun kallisto...

ADD REPLYlink modified 4 months ago by RamRS30k • written 4.5 years ago by frida.danielsson40

These are the transcriptomes they suggest to use: http://bio.math.berkeley.edu/kallisto/transcriptomes/

ADD REPLYlink written 4.5 years ago by WouterDeCoster44k
0
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

Removing the .1 shouldn't be a problem. Whether it's there or not is due to whether your files came from Ensembl or Gencode (or maybe UCSC) originally.

ADD COMMENTlink written 4.5 years ago by Devon Ryan96k

Ok, so you mean I can keep it?

ADD REPLYlink written 4.5 years ago by frida.danielsson40
1

That means you can remove it if it's causing problems.

ADD REPLYlink written 4.5 years ago by Devon Ryan96k
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