ERROR Cuffmerge for differential gene and expression analysis?

Question

[Kumar]

I am trying to use cufflinks-2.2.1.Linux_x86_64 for differential gene and expression analysis. First I used cufflinks with following command and got output files including transcripts.gtf. However, once I use cuffmerge I am getting an error. I am not sure if I installed it properly. please advice...

cufflinks ../sorted-SRR8136652.bam -o ../SRR8136652-cuff2.out

./cuffmerge -g ../Sus_scrofa.Sscrofa11.1.100.chr.gtf -s ../Sus_scrofa.Sscrofa10.2.dna.toplevel.fa -p 8 ../assemblies.txt

ERROR:

File "/usr/bin/cuffmerge", line 95 except getopt.error, msg: ^ SyntaxError: invalid syntax

[ATpoint]

Not helping with this problem itself, but is there a special reason you use such old software instead of more recent and maintained alternatives such as edgeR, limma or DESeq2?

[Kumar]

Thank you for letting me know. I am doing first time such type of analysis. There is no special reason. I have alignment output files .sam and .bam files from HASAT2. I also have feature count .txt file from FeatureCounts (http://subread.sourceforge.net/).

Now I am looking for differential gene and expression analysis. Please advice which pipelines should I use for this analysis.

[ATpoint]

Check the DESeq2 workflow. It is an R package that is available via Bioconductor with excellent documentation. http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

[Kristoffer Vitting-Seerup]

Here is a link for a short description on what quantification options you have with RNASeq data. It all depends on your questions :-)