Hi All,
I'm having a reoccurance of the "Error: this SAM file doesn't appear to be correctly sorted!" issue..
tophat 1.2.0 and cufflinks 1.0.2
bam file created using tophat
In cufflinks:
I'm having a reoccurance of the "Error: this SAM file doesn't appear to be correctly sorted!" issue..
tophat 1.2.0 and cufflinks 1.0.2
bam file created using tophat
Code:
/home/matthew/tophat-1.2.0/tophat -o /media/hd/annotation/tophat/social -r 100 -p 8 --allow-indels --library-type fr-unstranded /media/hd/annotation/tophat/bowtie.index.26May11.tuco.mrna /media/hd/tuco/mrna/trimmed/apache.final.clip_1.fq,/media/hd/tuco/mrna/trimmed/ep.final.clip_1.fq /media/hd/tuco/mrna/trimmed/apache.final.clip_2.fq,/media/hd/tuco/mrna/trimmed/ep.final.clip_2.fq
Code:
/home/matthew/cufflinks-1.0.2/cufflinks -o /media/hd/annotation/tophat/solitary/cufflinks --num-importance-samples 5000 --max-mle-iterations 20000 -p 16 /media/hd/annotation/tophat/solitary/accepted_hits.bam You are using Cufflinks v1.0.2, which is the most recent release. [18:04:56] Inspecting reads and determining fragment length distribution. > Processing Locus 10034_gs536_ge1663_3u1664_E [ ] 0% Error: this SAM file doesn't appear to be correctly sorted! current hit is at 10036_gs2_ge544_3u545_GENSCAN00000013565_Pteropus_neurexin:0, last one was at 10035_gs2_ge1360_ENSPTRP00000059044_PREDICTED::1331 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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