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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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merged.gtf file not working with FEELnc #32

Closed Tichaboni closed 5 years ago

Tichaboni commented 6 years ago

Hi @tderrien @vwucher @flegeai I have used your program with individual gtf files generated using cufflinks and it is working alright. I have used cuffmerge to combine different gtf files (technical replicates) but the merged.gtf file does not produce an output in the filter module. It creates an empty candidate_lncRNA.gtf file.

head merged.gtf

chr1    Cufflinks   exon    70097   70162   .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "HCLS1"; oId "NM_001031401"; nearest_ref "NM_001031401"; class_code "="; tss_id "TSS1"; p_id "P1";
chr1    Cufflinks   exon    72159   72242   .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "HCLS1"; oId "NM_001031401"; nearest_ref "NM_001031401"; class_code "="; tss_id "TSS1"; p_id "P1";
chr1    Cufflinks   exon    73496   73569   .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "HCLS1"; oId "NM_001031401"; nearest_ref "NM_001031401"; class_code "="; tss_id "TSS1"; p_id "P1";
chr1    Cufflinks   exon    73697   73826   .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "HCLS1"; oId "NM_001031401"; nearest_ref "NM_001031401"; class_code "="; tss_id "TSS1"; p_id "P1";

.....truncated.. What do I need to do to proceed with the merged file?

Thanks.

tderrien commented 5 years ago

Hi @Tichaboni ,

Sorry for the late reply. Did you manage to use your merged file within FEELnc? If no, could you tell us the parameters used for the filter module? Best

Thomas