## User: HKS

HKS0
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Status:
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Last seen:
4 months, 4 weeks ago
Joined:
5 months, 2 weeks ago
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d********@gmail.com

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#### Posts by HKS

<prev • 6 results • page 1 of 1 • next >
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... Yes got it.. the default value for readLength in tximport is 75. Thank you .. ...
written 5 months ago by HKS0
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... 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 5 months ago by HKS0
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... Will it be : 336.726562 * (9116157-9067712)/ 4844 ?? but this result does not match to the tximport output tx\$counts.. ...
written 5 months ago by HKS0
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...  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 5 months ago by HKS0 • updated 5 months ago by Michael Love24k
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... 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 5 months ago by HKS0
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... 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 ...
written 5 months ago by HKS0 • updated 5 months ago by James W. MacDonald50k

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