Entering edit mode
3 months ago
Nelo
▴
20
I'm currently working on RNA-seq data and have used HISAT2 for read alignment. I need to accurately determine the number of unique mapped reads. Here’s a summary of the information I have got:
cat SRR6821835_summary.txt
32710679 reads; of these:
32710679 (100.00%) were paired; of these:
4738072 (14.48%) aligned concordantly 0 times
26649415 (81.47%) aligned concordantly exactly 1 time
1323192 (4.05%) aligned concordantly >1 times
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4738072 pairs aligned concordantly 0 times; of these:
114451 (2.42%) aligned discordantly 1 time
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4623621 pairs aligned 0 times concordantly or discordantly; of these:
9247242 mates make up the pairs; of these:
8025125 (86.78%) aligned 0 times
1128235 (12.20%) aligned exactly 1 time
93882 (1.02%) aligned >1 times
87.73% overall alignment rate
My Questions is:
Is the count of reads aligned "concordantly exactly 1 time" in the HISAT2 summary file the correct measure of unique mapped reads?