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only one sample's FPKM value..?

Usually, I can get FPKM from cuffdiff & cufflinks.

If I have a only one sample, how can I get the FPKM value?

rna-seq
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updated by Ram Ram • written by leenaehyeon • leenaehyeon

1 answer

Cufflinks, rsem, kallisto, etc.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

I tried

cufflinks -M hg19.gtf --library-type fr-firststrand -o cufflinks_out tophat_out/A_accepted.hits.bam

Then, message was

[09:29:59] Loading reference annotation'
[09:30:01] Inspecting reads and determining fragment length distribution
>Processing Locus gi|387825349 [                             ]0%

Is that right? I waiting for 3hours.. but nothing happened

:(

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updated by Ram Ram • written by leenaehyeon • leenaehyeon

Cufflinks isn't known for being fast. You might instead try cuffquant.

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written by Devon Ryan Devon Ryan

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