Question: only one sample's FPKM value..?
0
gravatar for leenaehyeon
3.6 years ago by
leenaehyeon10
Korea, Republic Of
leenaehyeon10 wrote:

Usually, I can get FPKM from cuffdiff & cufflinks.

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

rna-seq • 1.3k views
ADD COMMENTlink modified 3.6 years ago by Devon Ryan90k • written 3.6 years ago by leenaehyeon10
0
gravatar for Devon Ryan
3.6 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

Cufflinks, rsem, kallisto, etc.

ADD COMMENTlink written 3.6 years ago by Devon Ryan90k

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 happend

:(

 

ADD REPLYlink written 3.6 years ago by leenaehyeon10

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

ADD REPLYlink written 3.6 years ago by Devon Ryan90k
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