Simon,
I have mapped reads with TopHat and then compared the exon counts from both HTseq and Partek method. There are 2x mapped reads found with Partek compared to HTseq-count. Some of the mRNAs show about the same number of counts for both methods. However, most show big differences.
Partek HTSeq-both strands
gene title cDNA+ cDNA- Column 1 cDNA+ cDNA-
MUC16 11 263 MUC16 14 299
DIFFERENT:
RHOU 89 714.678 RHOU 0 23
MUC12 20 283 MUC12 4 73
TTN 6.95E-05 268.507 TTN 9 464
Can you suggest how to a way to know why they differ?
Thanks,
Lana
I have mapped reads with TopHat and then compared the exon counts from both HTseq and Partek method. There are 2x mapped reads found with Partek compared to HTseq-count. Some of the mRNAs show about the same number of counts for both methods. However, most show big differences.
Partek HTSeq-both strands
gene title cDNA+ cDNA- Column 1 cDNA+ cDNA-
MUC16 11 263 MUC16 14 299
DIFFERENT:
RHOU 89 714.678 RHOU 0 23
MUC12 20 283 MUC12 4 73
TTN 6.95E-05 268.507 TTN 9 464
Can you suggest how to a way to know why they differ?
Thanks,
Lana
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