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Old 06-15-2016, 04:31 PM   #1
Beyounique
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Default HISAT2 reads aligned concordantly exactly 1 time

Hi all,

I am currently using HISAT2 to do read mapping. After having the mapped results, I am planning to only use reads aligned concordantly exactly 1 time (my data is paired-end RNA-seq data). I was wondering how does HISAT2 define reads aligned concordantly exactly 1 time?

Based on the website (https://ccb.jhu.edu/software/hisat2/manual.shtml), if I understand correctly, reads with YT:Z:CP and YT:Z:CP should be the reads aligned concordantly exactly 1 time. But the number I got doesn't match the number from HISAT2 log file. Below is the code I used and HISAT2 log file:

samtools view my_bam_file_after_mapping.bam | grep -e "\<NH:i:1\>" | grep -e "\<YT:Z:CP\>" > unique.mapped.sam

46673323 reads; of these:
46673323 (100.00%) were paired; of these:
17943238 (38.44%) aligned concordantly 0 times
22435343 (48.07%) aligned concordantly exactly 1 time
6294742 (13.49%) aligned concordantly >1 times
61.56% overall alignment rate

Here is the code I used to count the number of reads:
cat unique.mapped.sam | wc -l
The number I got is 53948500, which is a lot larger than 22435343.

Anyone had any idea on this one? Thank you very much!
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Old 05-18-2017, 08:34 AM   #2
metheuse
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Did you find the answer? I have the same question.
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Old 05-18-2017, 04:03 PM   #3
Beyounique
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No, I didn't find the answer...
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