Problem with running Cufflinks
Hi everyone, After mapping my RNA-seq data to the reference transcriptome using Bowtie, I tried to run Cufflinks, but got the following error message. It seems that I need to sort the SAM file got from Bowtie mapping. Dose anyone know how to solve this problem? Many thanks! Error running cufflinks. return code = 1 cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks) Command line: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 /galaxy/main_pool/pool4/files/004/761/dataset_4761476.dat [bam_header_read] EOF marker is absent. [bam_header_read] invalid BAM binary header (this is not a BAM file). File /galaxy/main_pool/pool4/files/004/761/dataset_4761476.dat doesn't appear to be a valid BAM file, trying SAM... [03:31:18] Inspecting reads and determining fragment length distribution. Error: this SAM file doesn't appear to be correctly sorted! current hit is at CGI_10025607:534, last one was at CGI_10021217:812 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. Yan
Hello Yan, This workflow can be used to sort SAM input for Cufflinks: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 Best, Jen Galaxy team On 8/10/12 3:13 AM, Yan He wrote:
Hi everyone,
After mapping my RNA-seq data to the reference transcriptome using Bowtie, I tried to run Cufflinks, but got the following error message. It seems that I need to sort the SAM file got from Bowtie mapping. Dose anyone know how to solve this problem? Many thanks!
*Error running cufflinks. return code = 1 cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks) Command line: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 /galaxy/main_pool/pool4/files/004/761/dataset_4761476.dat [bam_header_read] EOF marker is absent. [bam_header_read] invalid BAM binary header (this is not a BAM file). File /galaxy/main_pool/pool4/files/004/761/dataset_4761476.dat doesn't appear to be a valid BAM file, trying SAM... [03:31:18] Inspecting reads and determining fragment length distribution.
Error: this SAM file doesn't appear to be correctly sorted! current hit is at CGI_10025607:534, last one was at CGI_10021217:812 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.*
Yan
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Yan He