Quality Control After Alignment

Question

[asumani]

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?

Answer 1

[asumani]

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.