Question: how to interpret hisat2 result
0
gravatar for fatimarasool135
13 months ago by
fatimarasool13550 wrote:

Hi, I have run the HISAT2 tool for alignment. The tool was run successfully but can't understand the result's summary. I want to know two information from this summary as uniquely aligned reads and multi-mapped reads. how can i get these value? The summary of my work as

50646812 reads; of these:
50646812 (100.00%) were paired; of these:
8197826 (16.19%) aligned concordantly 0 times
39079594 (77.16%) aligned concordantly exactly 1 time
3369392 (6.65%) aligned concordantly >1 times
----
8197826 pairs aligned concordantly 0 times; of these:
2571448 (31.37%) aligned discordantly 1 time
----
5626378 pairs aligned 0 times concordantly or discordantly; of these:
11252756 mates make up the pairs; of these:
6125671 (54.44%) aligned 0 times
3906256 (34.71%) aligned exactly 1 time
1220829 (10.85%) aligned >1 times
93.95% overall alignment rate
rna-seq alignment assembly • 741 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by fatimarasool13550

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 13 months ago by WouterDeCoster43k

Hi WouterDeCoster,
Thank you. but each information is three times such as aligned concordantly exactly 1 time is three times in my summary, then how can conclude this result? What will the result/%of uniquely mapped reads?

ADD REPLYlink written 13 months ago by fatimarasool13550

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to the original question.

ADD REPLYlink written 13 months ago by genomax83k
1
gravatar for WouterDeCoster
13 months ago by
Belgium
WouterDeCoster43k wrote:

I want to know two information from this summary as uniquely aligned reads and multi-mapped reads. how can i get these value?

uniquely aligned reads: aligned exactly 1 time
multi-mapped reads: aligned >1 times

concordantly: paired-end reads are oriented as expected
discordantly: paired-end reads are oriented unexpected

ADD COMMENTlink written 13 months ago by WouterDeCoster43k

Hi WouterDeCoster, Thank you. but each information is three times such as aligned concordantly exactly 1 time is three times in my summary, then how can conclude this result? What will the result/%of uniquely mapped reads?

ADD REPLYlink written 13 months ago by fatimarasool13550

The summary mentions both pairs and individual reads.

ADD REPLYlink written 13 months ago by WouterDeCoster43k

Hi WouterDeCoster, I can say that in my data set,

Total number of reads is 5064681 in which

uniquely aligned reads is 39079594 (77.16%)
multi-mapped reads is 3369392 (6.65%)

can you please tell me I am correct for getting information about reads in my data summary?

ADD REPLYlink written 13 months ago by fatimarasool13550
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1701 users visited in the last hour