SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bug? duplicated genes in cufflinks output genes.expr silin284 Bioinformatics 3 05-17-2014 11:19 PM
Determine Top 100 Differentially Expressed Genes wilson90 Bioinformatics 1 07-08-2013 04:53 AM
comparing Bowtie/DESeq and Top-Hat/Cufflinks results maryb Bioinformatics 5 03-13-2012 07:46 AM
Cufflinks merging nearby genes xinchen Bioinformatics 2 01-24-2011 06:28 PM
Cufflinks merges adjacent genes proteomania Bioinformatics 1 11-20-2010 02:58 PM

Reply
 
Thread Tools
Old 02-08-2015, 04:40 PM   #1
reuben.jacob
Junior Member
 
Location: Adelaide, Australia

Join Date: Aug 2014
Posts: 3
Smile Cufflinks - top 100 genes

Dear All,

I'm new to RNA-Seq and Bioinformatics. We have done a RNA-Seq study using Illumina Hi-Seq (paired-end, 90bp reads) on two cell types.

I have managed to remove the adapters, trim low quality reads and remove reads < 50bp (Trim Galore). I have then mapped them (TopHat-v2.0.8b) and assembled the mapped reads (Cufflinks).

Is there a way to sort the transcripts.gtf file based on fpkm values to look for the top 100 highly expressed genes? (to make sure that the house-keeping genes/ genes that we know to be highly expressed are indeed highly expressed)

Any help would be much appreciated!

Cheers!
reuben.jacob is offline   Reply With Quote
Old 02-08-2015, 05:44 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,885
Default

It is not clear if you are using a known GTF file. If you only want to see the top 100 genes then you could use a read counting program like featureCounts to get real counts for your samples.

But if you just want to quickly see FPKM values in transcript.gtf files from cufflinks then try this. High FPKM values will be at the end of the display.

Code:
$ cut -f 9 transcripts.gtf | awk -F'"' '{print $2,"\t", $8}' | uniq | sort -s -k2n

Last edited by GenoMax; 02-08-2015 at 06:03 PM.
GenoMax is offline   Reply With Quote
Old 02-18-2015, 04:25 PM   #3
reuben.jacob
Junior Member
 
Location: Adelaide, Australia

Join Date: Aug 2014
Posts: 3
Smile

Sorry for the late reply! Thank you very much GenoMax! I just used the code and its what I needed. Really appreciate it! Cheers
reuben.jacob is offline   Reply With Quote
Old 02-18-2015, 05:04 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,885
Default

You are welcome. Thanks for the confirmation that the code worked.
GenoMax is offline   Reply With Quote
Reply

Tags
cufflinks, fpkm, gtf, highly expressed genes, illumina hiseq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:18 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO