User: HKS

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HKS0
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Posts by HKS

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Comment: C: tximport question on the values contained in "counts" and "abundance" matrices
... Yes got it.. the default value for readLength in tximport is 75. Thank you .. ...
written 4 weeks ago by HKS0
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Comment: C: tximport question on the values contained in "counts" and "abundance" matrices
... yes, i have used the Stringtie argument in tximport: So as you mentioned counts will be calculated by cov * average transcript length / read length so for this gene will it be : 336.726562*4844/? the answer in the output file is : 21748.3891418267 I just want to understand how it is calculated a ...
written 4 weeks ago by HKS0
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Comment: C: tximport question on the values contained in "counts" and "abundance" matrices
... Will it be : 336.726562 * (9116157-9067712)/ 4844 ?? but this result does not match to the tximport output tx$counts.. ...
written 4 weeks ago by HKS0
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Comment: C: tximport question on the values contained in "counts" and "abundance" matrices
... ``` t_id chr strand start end t_name num_exons length gene_id gene_name cov FPKM 15869 chr12 - 9067712 9116157 ENST00000318602.11 36 4844 ENSG00000175899.14 A2M 336.726562 134.45993 15870 chr12 - 9110314 9116229 ENST00000404455.2 6 623 ENSG00000175899.14 A2M 0.041283 0.016485 ``` ...
written 4 weeks ago by HKS0 • updated 4 weeks ago by Michael Love22k
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Comment: A: tximport question on the values contained in "counts" and "abundance" matrices
... Thanks for your answer: I have a question: t_id chr strand start end t_name num_exons length gene_id gene_name cov FPKM 15869 chr12 - 9067712 9116157 ENST00000318602.11 36 4844 ENSG00000175899.14 A2M 336.726562 134.45993 15870 chr12 - 9110314 9116229 ENST00000404455.2 6 623 ENSG00000175899.14 A2M ...
written 4 weeks ago by HKS0
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tximport question on the values contained in "counts" and "abundance" matrices
... I want to ask you about the matrices that are generated when using txOut = FALSE (default) because I want the values from StringTie quantification but gene level summarized (as they are more robust). I am using "StringTie" output files "t_data.ctab" as input files for tximport. tximport gives the li ...
tximport written 7 weeks ago by HKS0 • updated 4 weeks ago by James W. MacDonald49k

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