1. transcripts1.gtf , transcripts2.gtf , ... , transcripts20.gtf were produced by cufflinks.
2. I combined all of the gtf file to make my own annotation file, new.combined.gtf
cuffcompare -o new original.gtf transcripts1.gtf transcripts2.gtf ... transcripts20.gtf
3. I want to use HTSeq-count, by using new.combined.gtf.
However, in new.combined.gtf, among gene_id and oID and transcript_id and tss_id, which one do I have to choose? My thought is to use oID or tssID. But some reads that have different oId share the same tssID. In other words, some reads that have been previously annotated and other reads that have not been annotated have different oID but the same tssID.
Q: My goal is to see differentially expressed genes across the five different time points. To achieve this goal, when using HTSeq-count, which id is reasonable to choose as option?
Thank you in advance!
The below is the new.combined.gtf.
2. I combined all of the gtf file to make my own annotation file, new.combined.gtf
cuffcompare -o new original.gtf transcripts1.gtf transcripts2.gtf ... transcripts20.gtf
3. I want to use HTSeq-count, by using new.combined.gtf.
However, in new.combined.gtf, among gene_id and oID and transcript_id and tss_id, which one do I have to choose? My thought is to use oID or tssID. But some reads that have different oId share the same tssID. In other words, some reads that have been previously annotated and other reads that have not been annotated have different oID but the same tssID.
Q: My goal is to see differentially expressed genes across the five different time points. To achieve this goal, when using HTSeq-count, which id is reasonable to choose as option?
Thank you in advance!
The below is the new.combined.gtf.
Mt:3452:Mt3.5.1Chr1 E exon 154859 155160 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "Medtr1g005010.1"; tss_id "TSS1";
Mt:3452:Mt3.5.1Chr1 E exon 155201 161330 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 E exon 161501 161880 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 E exon 162000 162267 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "3"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 E exon 162314 162479 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "4"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 161506 162151 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00004880"; exon_number "1"; oId "CUFF.2.1"; tss_id "TSS4";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 162327 162630 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00004881"; exon_number "1"; oId "CUFF.2.1"; tss_id "TSS5";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 174216 175572 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00007444"; exon_number "1"; oId "CUFF.9.1"; tss_id "TSS6";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 188340 188516 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00007444"; exon_number "2"; oId "CUFF.9.1"; tss_id "TSS6";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 175331 175619 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00014784"; exon_number "1"; oId "CUFF.5.1"; tss_id "TSS8";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 176045 176603 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00004882"; exon_number "1"; oId "CUFF.8.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 176728 177280 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00004882"; exon_number "2"; oId "CUFF.8.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 177480 177481 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00004882"; exon_number "3"; oId "CUFF.8.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 176052 177755 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00007445"; exon_number "1"; oId "CUFF.10.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 E exon 176184 176603 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000003"; exon_number "1"; oId "Medtr1g005100.1"; tss_id "TSS10";
Mt:3452:Mt3.5.1Chr1 E exon 176728 176892 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000003"; exon_number "2"; oId "Medtr1g005100.1"; tss_id "TSS10";
Mt:3452:Mt3.5.1Chr1 E exon 177155 177280 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000003"; exon_number "3"; oId "Medtr1g005100.1"; tss_id "TSS10";
Mt:3452:Mt3.5.1Chr1 E exon 155201 161330 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 E exon 161501 161880 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 E exon 162000 162267 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "3"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 E exon 162314 162479 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "4"; oId "Medtr1g005020.1"; tss_id "TSS2";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 161506 162151 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00004880"; exon_number "1"; oId "CUFF.2.1"; tss_id "TSS4";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 162327 162630 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00004881"; exon_number "1"; oId "CUFF.2.1"; tss_id "TSS5";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 174216 175572 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00007444"; exon_number "1"; oId "CUFF.9.1"; tss_id "TSS6";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 188340 188516 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00007444"; exon_number "2"; oId "CUFF.9.1"; tss_id "TSS6";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 175331 175619 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00014784"; exon_number "1"; oId "CUFF.5.1"; tss_id "TSS8";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 176045 176603 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00004882"; exon_number "1"; oId "CUFF.8.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 176728 177280 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00004882"; exon_number "2"; oId "CUFF.8.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 177480 177481 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00004882"; exon_number "3"; oId "CUFF.8.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 Cufflinks exon 176052 177755 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00007445"; exon_number "1"; oId "CUFF.10.1"; tss_id "TSS9";
Mt:3452:Mt3.5.1Chr1 E exon 176184 176603 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000003"; exon_number "1"; oId "Medtr1g005100.1"; tss_id "TSS10";
Mt:3452:Mt3.5.1Chr1 E exon 176728 176892 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000003"; exon_number "2"; oId "Medtr1g005100.1"; tss_id "TSS10";
Mt:3452:Mt3.5.1Chr1 E exon 177155 177280 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000003"; exon_number "3"; oId "Medtr1g005100.1"; tss_id "TSS10";
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