hi
i used bowtie -->samtools 0.1--->cufflinks
i did cufflinks for each dataset and i got all the four files as a result
but the resulting gene.fpkm.tracking file looks like this
tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status gene0 - - gene0 DDX11L1 - NC_000001.11:11873-14409 - - 0 0 0 OK gene1 - - gene1 WASH7P - NC_000001.11:14361-29370 - - 0 0 0 OK gene2 - - gene2 MIR6859-1 - NC_000001.11:17368-17436 - - 0 0 0 OK gene3 - - gene3 LOC107985730 - NC_000001.11:29925-31295 - - 0 0 0 OK gene4 - - gene4 MIR1302-2 - NC_000001.11:30365-30503 - - 0 0 0 OK gene5 - - gene5 FAM138A - NC_000001.11:34610-36081 - - 0 0 0 OK CUFF.1 - - CUFF.1 LOC105379212,OR4G4P - NC_000001.11:51942-53959 - - 0 0 0 OK gene8 - - gene8 OR4G11P - NC_000001.11:63015-63885 - - 0 0 0 OK gene9 - - gene9 OR4F5 - NC_000001.11:69090-70008 - - 0 0 0 OK CUFF.2 - - CUFF.2 LOC100996442,RNU6-1100P - NC_000001.11:91168-267354 - - 0 0 0 OK gene15 - - gene15 GTF2IP10 - NC_000001.11:164688-164792 - - 0 0 0 OK gene11 - - gene11 SEPT14P18 - NC_000001.11:126645-129225 - - 0 0 0 OK gene12 - - gene12 CICP27 - NC_000001.11:131067-134836 - - 0 0 0 OK gene13 - - gene13 LOC729737 - NC_000001.11:134772-140566 - - 0 0 0 OK gene16 - - gene16 LOC102725121 - NC_000001.11
*the transcript.gtf file*
NC_000001.11 Cufflinks transcript 11874 14409 1 + . gene_id "gene0"; transcript_id "rna0"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no"; NC_000001.11 Cufflinks exon 11874 12227 1 + . gene_id "gene0"; transcript_id "rna0"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; NC_000001.11 Cufflinks exon 12613 12721 1 + . gene_id "gene0"; transcript_id "rna0"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; NC_000001.11 Cufflinks exon 13221 14409 1 + . gene_id "gene0"; transcript_id "rna0"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; NC_000001.11 Cufflinks transcript 14362 29370 1 - . gene_id "gene1"; transcript_id "rna1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no"; NC_000001.11 Cufflinks exon 14362 14829 1 - . gene_id "gene1"; transcript_id "rna1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; NC_000001.11 Cufflinks exon 14970 15038 1 - . gene_id "gene1"; transcript_id "rna1"; exon_number "2"; FPKM
and the isoforms.fpkm file
tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status rna0 - - gene0 DDX11L1 - NC_000001.11:11873-14409 1652 0 0 0 0 OK rna1 - - gene1 WASH7P - NC_000001.11:14361-29370 1769 0 0 0 0 OK rna3 - - gene2 MIR6859-1 - NC_000001.11:17368-17391 23 0 0 0 0 LOWDATA rna2 - - gene2 MIR6859-1 - NC_000001.11:17368-17436 68 0 0 0 0 OK rna4 - - gene2 MIR6859-1 - NC_000001.11:17408-17431 23 0 0 0 0 LOWDATA rna5 - - gene3 LOC107985730 - NC_000001.11:29925-31295 538 0 0 0 0 OK rna6 - - gene4 MIR1302-2 - NC_000001.11:30365-30503 138 0 0 0 0 OK rna7 - - gene4 MIR1302-2 - NC_000001.11:30437-30458
all the values are zero
why is it so ?..can u help..
thank u in advance
