Entering edit mode
3.7 years ago
hemantcnaik
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0
Hello I have mapped my single cell data using STAR aligner with the mouse mm10 genome mapping percentage when I run multiqc its showing on average 40-50%. can any one suggest me is it good to go for further analysis or I have to pass any more threshold for mapping.
Thank you.
Not answering your question but pointing out some relevant points in case you have not thought about them.
Allele specific mapping is tricky at best even with bulk RNAseq data. I am not sure how single cell data would do. You do need to keep in mind that aligners will align reads with 1+ errors (which could be the locations of the alleles, unless you are using perfect matching) so alignments you currently have may not be usable for allele specific expression. If the mice you have are not the standard black 6 then that adds another level of complexity since genomes of your mice may not be the same as the reference.
Adding on this, the mapping % is not unusual for single-cell data in my experience. Be aware that many sc technologies are 3' tagged so you only get a tiny fraction of the entire gene and in this tiny fraction there need to be SNPs that distinguish alleles. I would see if there are published pipelines that were tailored for what you want to do. Don't try to build a custom pipeline. As genomax says allel specificity is challenging enough for high coverage RNA-seq. You need something that is robust and therefore specifically developed for sc data.
Helo thanks for your response can you please mention any published pipelines it will be very helpfull
@ATpoint @genomax Thanks for the reply. Can you please mention any paper or any specific tool for single cell allelic analysis because I am planning to use GATK allelecounter with the defualt parameter. and got doubt mapping may infer the data analysis so just wanted to clarify. and I am only selecting SNPs that distinguish alleles