How to Accurately Determine Unique Mapped Reads from HISAT2 Output summary file
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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
    ----
    4738072 pairs aligned concordantly 0 times; of these:
      114451 (2.42%) aligned discordantly 1 time
    ----
    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?

mapped unique analysis Hisat2 RNA-seq • 187 views
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