Blog:Found odd bug with cufflinks

Question

[Anna S]

Hello,

This is not a question but just a comment. I found an odd bug with cufflinks 2.2.1 just now! I've been using cuflfinks extensively and this is the first time I've run into it. I don't know if later versions of cufflinks fix this problem.

In particular, all of the transcripts in the transcripts.gtf file produced by cufflinks were fine, except for one that had "Cufflinks" in the 4th field, and one that had "Cufflinks" in the 5th field as seen below, which caused a subsequent cuffmerge command to fail. Once I removed these 2 offending lines, cuffmerge seems to be working now.

11      Cufflinks       ex11    Cufflinks       transcript      87405065        87555823        1       +       .       gene_id "CUFF.1518"; transcript_id "ENSMUST00000060835"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no";
13      Cufflinks       transcript      213     Cufflinks       transcript      23456992        23465875        1000    -       .       gene_id "ENSMUSG00000000706"; transcript_id "ENSMUST00000041674"; FPKM "0.0434702236"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.652053"; cov "0.001153"; full_read_support "no";

[cmdcolin]

I'd add this to their github issues page if possible. That is certainly weird