Question: How to build genome index file with ERCC (spike-in )
0
gravatar for Mike
4 weeks ago by
Mike1.1k
UK
Mike1.1k wrote:

Hi all,

I have GRCh37 fasta sequence & GTF annotation file and ERCC fasta sequence file (but I don’t have ERCC annotation file (GTF)). I want to build genome index file including ERCC sequence using STAR. please help me how to build index file with ERCC?

Thanks

sequence annotation genome • 122 views
ADD COMMENTlink modified 4 weeks ago by Devon Ryan88k • written 4 weeks ago by Mike1.1k
2
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

Cat the fasta files together and then add an entry for each spike-in into the GTF file. Note that you could instead just map against the spike-ins and use samtools idxstats to get the counts for the spike-ins. The multimapping rate within the spike-ins and between the spike-ins and the human genome will be very low, so this will produce accurate enough results.

ADD COMMENTlink written 4 weeks ago by Devon Ryan88k

Thanks Devon, Sorry, how to add entry for each spike-in into the GTF file?

ADD REPLYlink written 4 weeks ago by Mike1.1k

It's a text file, open it in your editor of choice.

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

Thanks, Sorry for again, but I don't have annotation information for spike-ins. Can I add only spike-in names ?

ADD REPLYlink written 4 weeks ago by Mike1.1k
1

The annotation is the name and entire length, which you can get from the fasta file.

ADD REPLYlink written 4 weeks ago by Devon Ryan88k
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