Question: how to interpret hisat2 result
0
gravatar for fatimarasool135
5 weeks ago by
fatimarasool13520 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 • 145 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by fatimarasool13520

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ADD REPLYlink written 5 weeks ago by WouterDeCoster39k

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 5 weeks ago by fatimarasool13520

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 5 weeks ago by genomax67k
1
gravatar for WouterDeCoster
5 weeks ago by
Belgium
WouterDeCoster39k 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 5 weeks ago by WouterDeCoster39k

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 5 weeks ago by fatimarasool13520

The summary mentions both pairs and individual reads.

ADD REPLYlink written 5 weeks ago by WouterDeCoster39k

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 4 weeks ago by fatimarasool13520
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