Alignment query

Question

[Komal]

hello everyone, is it ok 65 % alignment rate for transcriptome rna analysis ?

[GenoMax]

is it ok 65 % alignment rate for transcriptome rna analysis ?

There is not enough information in this one-line question to provide a useful answer. Please include additional information about what kind of data this is, which program was used for alignments/mapping etc.

[Komal]

heptacellular cancer data i did alignment from hisat2 aligner

[GenoMax]

Assuming you have done everything right this may be what you will have to work with. Check with PCA to make sure there are no outliers.

Answer 1

[Istvan Albert]

Ideally, one would expect a rate closer to 95% - but you should really visualize the alignments and see how it aligns relative to exons and introns.

You should see clear delineation at the exon boundaries and minimal mapping in intergenic regions.

That would be the most appropriate way to determine the quality of data.