Gene Count Matrix

Question

[chimerajit]

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?

[JC]

How are you generating your count matrix? Seems you are counting reads mapped >1 time.

[chimerajit]

Sorry for late reply. I generated count using stringtie.