Question: How to understand Hisat2 aligment result
0
gravatar for Bioinfonext
20 months ago by
Bioinfonext110
Korea
Bioinfonext110 wrote:

I map pair end read using Hisat2 to genome:

[root@psgl hisat2]# /home/yog/software/hisat2-2.0.4/hisat2 -p 8 -x Radish_index -1

/data/SNU_work/Analysis/unmapped/unmapped/hisat2/unmap_Read1.fastq -2

/data/SNU_work/Analysis/unmapped/unmapped/hisat2/unmap_Read2.fastq -S unmap.sam

Result:

101038635 reads; of these:

101038635 (100.00%) were paired; of these:

6478970 (6.41%) aligned concordantly 0 times

45018304 (44.56%) aligned concordantly exactly 1 time

49541361 (49.03%) aligned concordantly >1 times

----
6478970 pairs aligned concordantly 0 times; of these:

  338196 (5.22%) aligned discordantly 1 time

----
6140774 pairs aligned 0 times concordantly or discordantly; of these:

  12281548 mates make up the pairs; of these:

    5865219 (47.76%) aligned 0 times

    4078697 (33.21%) aligned exactly 1 time

    2337632 (19.03%) aligned >1 times

97.10% overall alignment rate

What is the meaning of aligned 0 times?

What is the meaning of aligned concordantly?

Please help!

rna-seq • 2.5k views
ADD COMMENTlink written 20 months ago by Bioinfonext110

See Devon's answer: tophat output files containing the reads which mapped uniquely as a pair

ADD REPLYlink written 20 months ago by genomax56k
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: 1061 users visited in the last hour