Question

only one sample's FPKM value..?

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8.5 years ago

leenaehyeon ▴ 10

Usually, I can get FPKM from cuffdiff & cufflinks.

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

RNA-Seq • 2.1k views

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.5 years ago by leenaehyeon ▴ 10

Ram · Answer 1 · 2015-10-14

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8.5 years ago

Devon Ryan 104k

Cufflinks, rsem, kallisto, etc.

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.5 years ago by Devon Ryan 104k

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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

:(

ADD REPLY • link updated 20 months ago by Ram 43k • written 8.5 years ago by leenaehyeon ▴ 10

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

ADD REPLY • link 8.5 years ago by Devon Ryan 104k