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Forum: RNA Sequencing 04-26-2017, 04:44 AM
Replies: 6
Views: 5,328
Posted By farri
The focus of my study is on fold change(FC)-based...

The focus of my study is on fold change(FC)-based evaluation of transcriptional changes, thus intra-gene comparison. I am interested in genes which are strongly differentially regulated between two...
Forum: RNA Sequencing 04-16-2017, 09:34 AM
Replies: 6
Views: 5,328
Posted By farri
Cuffnorm's FPKM - advisable to perform TPM conversion?

Hi,

I performed a detailed time-course mRNA-seq experiment without any sequencing replicates (the input RNA, however, was a pool of equal amounts of total RNA from biological replicates). As I...
Forum: RNA Sequencing 11-16-2015, 01:25 AM
Replies: 1
Views: 2,913
Posted By farri
I found a very simple solution myself: ...

I found a very simple solution myself:

gffread .../merged.gtf -o .../merged.gff
gffread .../merged.gff -g genome.fasta -w merged_transcripts.fasta
Forum: RNA Sequencing 11-09-2015, 05:18 AM
Replies: 1
Views: 2,913
Posted By farri
Cuffmerge - merged.gtf - gffread - empty file

Hi!

I am using the cufflinks cuffmerge workflow to assemble transcripts for in total 12 libraries. I now want to extract nucleotide sequences from the "merged.gft" file produced by cuffmerge, in...
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