Idong,
Did you use the --no-novel-juncs command?
Did you use the --no-novel-juncs command?
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cufflinks -G htt.gtf htt.sam
$ /home/dongx/bin/cufflinks-0.9.3.Linux_x86_64/cufflinks -G htt.gtf htt.sam /home/dongx/bin/cufflinks-0.9.3.Linux_x86_64/cufflinks: /usr/lib64/libz.so.1: no version information available (required by /home/dongx/bin/cufflinks-0.9.3.Linux_x86_64/cufflinks) [bam_header_read] EOF marker is absent. File htt.sam doesn't appear to be a valid BAM file, trying SAM... [17:33:52] Inspecting reads and determining fragment length distribution. > Processed 1 loci. [*************************] 100% > Map Properties: > Total Map Mass: 3542.44 > Read Type: 40bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 204.01 > Estimated Std Dev: 74.81 [17:33:52] Estimating transcript abundances. > Processed 1 loci. [*************************] 100%
$ cat genes.expr gene_id bundle_id chr left right FPKM FPKM_conf_lo FPKM_conf_hi status [COLOR="Red"]ENSG00000197386 3 chr4 3076406 3245676 0 0 0 OK[/COLOR]
[dongx@hpcc01 ~]$ cat transcripts.expr trans_id bundle_id chr left right FPKM FMI frac FPKM_conf_lo FPKM_conf_hi coverage length effective_length status ENST00000355072 3 chr4 3076406 3245676 0 0 0 0 0 0 13531 13531 OK ENST00000506137 3 chr4 3117054 3123439 0 0 0 0 0 0 784 784 OK ENST00000512909 3 chr4 3123125 3125193 0 0 0 0 0 0 613 613 OK ENST00000510626 3 chr4 3130064 3245667 0 0 0 0 0 0 14491 14491 OK ENST00000509618 3 chr4 3162087 3174954 0 0 0 0 0 0 432 432 OK ENST00000513639 3 chr4 3180072 3182400 0 0 0 0 0 0 261 261 OK ENST00000513326 3 chr4 3180072 3182514 0 0 0 0 0 0 375 375 OK ENST00000509043 3 chr4 3180072 3182521 0 0 0 0 0 0 382 382 OK ENST00000502820 3 chr4 3204731 3208306 0 0 0 0 0 0 290 290 OK ENST00000509751 3 chr4 3213637 3214782 0 0 0 0 0 0 725 725 OK ENST00000512068 3 chr4 3230370 3231649 0 0 0 0 0 0 403 403 OK ENST00000513806 3 chr4 3230438 3237123 0 0 0 0 0 0 436 436 OK ENST00000508321 3 chr4 3237149 3237906 0 0 0 0 0 0 388 388 OK
$cufflinks -G hg18_annotation.gtf MyFile.sam
[20:24:17] Inspecting reads and determining fragment length distribution. > Processing Locus chr6:27032750-27099732 [***************** ] 69% Error: this SAM file doesn't appear to be correctly sorted! current hit is at chr10:272501, last one was at chr9:139953334 Cufflinks requires that if your file has SQ records in the SAM header that they appear in the same order as the chromosomes names in the alignments. If there are no SQ records in the header, or if the header is missing, the alignments must be sorted lexicographically by chromsome name and by position.
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