Question: counting ERCCs spike-ins in RNAseq data
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alirezamomeni707 • 0 wrote:
I have used ERCC spike-in in my RNAseq data. I have aligned my data and now I have bam files. to count the reads per gene I used htseq-count(which needs gtf file). I also have to count ERCC (I have 98 spike-in). I have fasta file of ERCCs. do you know how I can count the ERCCs?
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modified 2.2 years ago
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Charles Plessy • 2.7k
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2.2 years ago by
alirezamomeni707 • 0
Ideally you could have appended the ERCC fasta to the genome and then aligned your data. Since you have not done that you would need to create a new "genome" (and a GTF file to go with it) and then align/count.
is it not possible to align to ERCC fasta and it's GTF post alignment (using aligned bam)? (aligned bam = aligned with reference fasta other than ERCC)
You can filter them out and quantify them with BBMap's Seal using the aligned bam.
Since ERCC sequences should be totally diverse it should not matter what you use.
thanks. actually I have aligned to ERCC (made index from fasta file). but I do not have GTF file for that. actually this is the main problem
You make one up yourself.