SEQanswers - Threads Tagged with cuffmerge

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Threads Tagged with cuffmerge

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Threads Tagged with cuffmerge
	Thread / Thread Starter	Last Post	Replies	Views	Forum
	Problems with cuffmerge ( 1 2) Nnogueira	06-25-2016 09:38 PM by Brian Bushnell	23	10,563	Bioinformatics
	biological replicates cuffmerge? KateShepard	04-28-2016 06:52 AM by KateShepard	3	1,168	RNA Sequencing
	Cuffdiff reporting same locus several times &/or more than one gene per transcript Marta123	11-25-2015 07:40 AM by Marta123	0	679	Bioinformatics
	Cuffmerge error cbaudo	11-25-2015 06:51 AM by alexGrenoble	3	1,644	Bioinformatics
	Cuffmerge - merged.gtf - gffread - empty file farri	11-16-2015 01:25 AM by farri	1	1,215	RNA Sequencing
	Reference annotation file (gtf) for the NOD/ShiltJ mouse? michelletran	09-15-2015 06:16 AM by dpryan	3	917	RNA Sequencing
	Cuffmerge loses gene_id annotation xavier.robin	08-21-2015 01:47 AM by xavier.robin	0	1,137	RNA Sequencing
	Differential expression using TopHat/Cufflinks, analysis by CumeRbund imsharmanitin	08-17-2015 08:57 AM by csmatyi	1	1,117	RNA Sequencing
	Cuffmerge error file never signals "done"...is this normal? asapp	07-10-2015 06:00 AM by asapp	2	755	Bioinformatics
	Cuffmerge error (GFaSeqGet): subsequence cannot be larger than nixstix	06-29-2015 09:07 AM by nixstix	0	899	RNA Sequencing
	Cufflinks problem barbarian	04-12-2015 12:31 AM by barbarian	0	1,190	Bioinformatics
	Tophat error with Cuffmerged GTF Kolamite	02-21-2015 09:05 AM by Kolamite	0	920	RNA Sequencing
	Cuffmerge outputs only exon annotation data gwilymh	02-03-2015 10:06 AM by gwilymh	0	903	Bioinformatics
	cuffmerge combining genes from adjacent loci?? beeman	12-10-2014 06:13 AM by dalesan	2	1,577	Bioinformatics
	cummeRbund - how to get gene name in diffData output ( 1 2) turnersd	10-17-2014 10:33 AM by david.eby	32	25,556	Bioinformatics
	cuffmerge samples from different strains or leave separate Sentinel156	10-08-2014 05:39 PM by Sentinel156	0	814	RNA Sequencing
	cuffdiff: use merged.gtf from cuffmerge or combined.gtf from cuffcompare? ( 1 2) turnersd	10-02-2014 03:41 AM by Gonza	21	30,128	Bioinformatics
	gffread to output sequence, gene_id not output daikon	09-25-2014 08:27 PM by daikon	2	2,215	RNA Sequencing
	New transcript? sindrle	09-11-2014 10:48 AM by rajarapupriya	1	871	RNA Sequencing
	Cuffmerge can't execute gtf_to_sam thickrick99	08-18-2014 11:34 AM by thickrick99	1	1,673	RNA Sequencing
	error in Cufflinks v2.0.2 when using Cuffmerge mattanswers	07-11-2014 02:40 PM by mattanswers	2	1,959	Bioinformatics
	Warning in CuffDiff when using novel transcripts from CuffMerge as input komalsrathi	06-02-2014 10:43 AM by komalsrathi	0	1,314	RNA Sequencing
	Warning in cuffmerge genome1	05-15-2014 10:01 AM by genome1	2	2,467	General
	Can't use my SAM files for cuffdiff jasminegirl18	02-18-2014 09:21 PM by jasminegirl18	8	1,561	Bioinformatics
	A question about FPKM value in the Tophat/Cufflinks pipeline baptist	12-22-2013 03:03 AM by baptist	0	1,429	RNA Sequencing
	Cuffmerge output with missing strand information, htseq-count error komalsrathi	11-27-2013 01:00 PM by dpryan	1	2,583	Bioinformatics
	cuffDiff "cannot open reference GTF file" gwilymh	11-19-2013 01:06 PM by liweixie	2	2,709	Bioinformatics
	cuffmerge assembly vs denovo assembly of RNAseq data skm	10-16-2013 09:16 PM by skm	0	1,535	Bioinformatics
	CuffDiff cannot opn BAM file made in TopHat gwilymh	09-12-2013 03:04 AM by dpryan	2	2,485	Bioinformatics
	Why does Cufflinks assign a strand to some RNA sequences but not others? gwilymh	09-05-2013 04:26 AM by kmcarr	1	1,741	Bioinformatics

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