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Cufflinks analysis for transcriptome assembly
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Stringtie and Cufflinks and Cuffmerge
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How to find novel gene/isoform in 1 RNA-SEQ sample?
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Error: duplicate GFF ID 'ENST00000400518' encountered! [FAILED] Error: could not execute cu…
written by PK •Hi folks, When I run cuffmerge I have used this command cufflinks Version - cufflinks_2_2_1 cuffmerge -p 16 -o ~/RNA_HOME/cuffmerge/merged -g ~/RNA_HOME/refs/hg19/genes/genes_chr22_ERCC92.gtf ~/RNA_HOME/de_novo/assembly_GTF_list.txt **Error: duplicate …
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How/when to use cuffmerge and/or cuffcompare?
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tophat-cufflinks command pipeline
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Cuffcompare: Some Cufflinks Transcripts Are Not Contained By Cuffcompare Output Tmap File
written by zju.whw •<p>I'm using the tophat/cufflinks/cuffcompare tools to deal with the RNAseq to assemble the transcriptome. When I use cuffcompare to compare Cufflinks transcript gtf file with …
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Rna-Seq With Cuffdiff: Use Merged.Gtf From Cuffmerge Or Combined.Gtf From Cuffcompare?
written by Stephen<p>Dear community,</p> <p>A similar question was <a href="http://seqanswers.com/forums/showthread.php?t=14453&highlight=cuffmerge+cuffcompare+cuffdiff">asked previously on SeqAnswers</a> and no answers were posted. I'll expand that question.</p> <p>I'm trying to better understand …
I believe (but might be wrong) that you have been told before that the pipeline tophat-cufflinks-cuffmerge is no longer the accepted best pipeline for RNA-seq analysis and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.)