Inquery: not-stranded transcripts ("." in strand column) in cufflinks output gtf file

sunfuhui · 11-15-2012, 03:43 PM

Hi, All

Could you please give me some suggestions about:
How to handle transcripts, in cufflinks output gtf file, whose strand column is marked as "." rather than "+/-", when I try to extract sequences based on gtf?

chr1 Cufflinks exon 160126969 160127906 . . . gene_id "XLOC_010604"; transcript_id "TCONS_00021170"; exon_number "1"; oId "CUFF.7826.1"; tss_id "TSS12746";
chr1 Cufflinks exon 160128793 160130000 . . . gene_id "XLOC_010605"; transcript_id "TCONS_00021171"; exon_number "1"; oId "CUFF.7827.1"; tss_id "TSS12747";
chr1 Cufflinks exon 160223473 160223719 . . . gene_id "XLOC_010606"; transcript_id "TCONS_00021172"; exon_number "1"; oId "CUFF.7829.1"; tss_id "TSS12748";

Thank you very much!!!!!!!

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11-15-2012, 03:43 PM	#1
sunfuhui Junior Member Location: athens, ga Join Date: Jul 2012 Posts: 8	Inquery: not-stranded transcripts ("." in strand column) in cufflinks output gtf file Hi, All Could you please give me some suggestions about: How to handle transcripts, in cufflinks output gtf file, whose strand column is marked as "." rather than "+/-", when I try to extract sequences based on gtf? chr1 Cufflinks exon 160126969 160127906 . . . gene_id "XLOC_010604"; transcript_id "TCONS_00021170"; exon_number "1"; oId "CUFF.7826.1"; tss_id "TSS12746"; chr1 Cufflinks exon 160128793 160130000 . . . gene_id "XLOC_010605"; transcript_id "TCONS_00021171"; exon_number "1"; oId "CUFF.7827.1"; tss_id "TSS12747"; chr1 Cufflinks exon 160223473 160223719 . . . gene_id "XLOC_010606"; transcript_id "TCONS_00021172"; exon_number "1"; oId "CUFF.7829.1"; tss_id "TSS12748"; Thank you very much!!!!!!!