Un-Stranded Transcripts In Cuffmerge Output; How To Extract Its Sequence?? Gffread?

Question

[sunfuhui1984]

Hi All,

Could you please give me some suggestions about:

How to handle transcripts, in cuffmerge output gtf file, whose strand column is marked as "." rather than "+/-", when I try to extract sequences based on gtf?

For example: 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";

I used gffread to extract the sequences, but found that gffread treats all "." as "+". Does it make sense????

What should I do? delete such kind of transcripts?

Thank you very much!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

[Devon Ryan]

It rather depends on what you plan to do with the resulting sequences.