Gene Count Matrix
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5 weeks ago
chimerajit • 0

I did paired end alignment with HiSat and the alignment log is telling

  • 22608754 reads; -of these: 22608754 (100.00%) were paired; of these:
    6129947 (27.11%) aligned concordantly 0 times
    3041428 (13.45%) aligned concordantly exactly 1 time
    13437379 (59.43%) aligned concordantly >1 times
    ----
    6129947 pairs aligned concordantly 0 times; of these:
      3806 (0.06%) aligned discordantly 1 time
    ----
    6126141 pairs aligned 0 times concordantly or discordantly; of these:
      12252282 mates make up the pairs; of these:
        11803075 (96.33%) aligned 0 times
        73963 (0.60%) aligned exactly 1 time
        375244 (3.06%) aligned >1 times
    
    73.90% overall alignment rate

I don't have problem with this

From above I understand this 22608754 x2 =45217508X0.73=330087809(aligned reads) but for same sample gene count matrix showing reads count total is 46513138. What makes this difference?

Genecount Hisat matrix Stringtie • 153 views
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How are you generating your count matrix? Seems you are counting reads mapped >1 time.

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