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Quality Control After Alignment

Hi all,

I have 95 bam files, scRNA-seq reads aligned to human genome. I used HISAT2 as I did for my other bulk RNA datasets. Yet, total alignment rate for scRNA-seq data ranges between 60%-90% after successful adapter trimming. Should I remove the samples which are below total 70% alignement rate? If yes, how can I do that? In the HISAT log file, sample names are not written,so I don't know which sample belongs to which rate. I guess it is the sample name order.

So, how can I proceed with this data?

quality control rna-seq hisat2 scrna-seq
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written by asumani asumani

1 answer

Just for the record, I used samtools flagstat to print out sample IDs and their alignment rates. Then after a little parsing, I removed the files I need to remove.

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written by asumani asumani

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