Gene Count Matrix
I did paired end alignment with HiSat and the alignment log is telling
- 22608754 reads;
-of these: 22608754 (100.00%) were paired; of these:
73.90% overall alignment rate6129947 (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
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?
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chimerajit •
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How are you generating your count matrix? Seems you are counting reads mapped >1 time.
Sorry for late reply. I generated count using stringtie.