HISAT2 Alignment Result

Question

[akashbala0]

Hi everyone,

I have aligned my RNAseq data in hisat2 and I am confused with the Alignment Result.

31749920 reads; of these:
31749920 (100.00%) were unpaired; of these:
199326 (0.63%) aligned 0 times
28419292 (89.51%) aligned exactly 1 time
3131302 (9.86%) aligned >1 times
99.37% overall alignment rate

As I'm working on DEG analysis I have 9.86% aligned more than one time. Is anything wrong with processing these data, can I proceed with this data.

[lieven.sterck]

why do you think this is not a valid result to continue for a DEG analysis?

[akashbala0]

Because 9.86% are aligned more than once.

[lieven.sterck]

and this for educational purposes :)

why do you think you need the ones that align more than once? (do you fully understand what that means?)

[GenoMax]

akashbala0 : Please do not delete threads that have received comments/answers. Deleting posts is not the way to indicate that a problem was solved. Accepting answer(s) is. You have already done that. Thanks!

Answer 1

[lieven.sterck]

sure, this is actually a good result!

for DEG you want as little multi mapping as possible, you need the unique ones, so yes, go ahead with this.

[akashbala0]

thank you @lieven.sterck