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Old 11-15-2012, 02:43 PM   #1
sunfuhui
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Location: athens, ga

Join Date: Jul 2012
Posts: 8
Default 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!!!!!!!
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