Hi,
I am using bowtie and cufflinks to get gene expression from RNA seq data.
My workflow is like this:
bowtie -p 4 --best --strata -m 1 --sam mm9/mm9 -q SRR032476.fastq SRR032476.sam
and when i run
cufflinks SRR032476.sam
I got an error like
the head of sam file is:
Anyone can help this? Thanks so much.
I am using bowtie and cufflinks to get gene expression from RNA seq data.
My workflow is like this:
bowtie -p 4 --best --strata -m 1 --sam mm9/mm9 -q SRR032476.fastq SRR032476.sam
and when i run
cufflinks SRR032476.sam
I got an error like
Code:
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks) [bam_header_read] EOF marker is absent. File SRR032476.sam doesn't appear to be a valid BAM file, trying SAM... [15:46:53] Inspecting reads and determining fragment length distribution. > Processing Locus chr2:131113838-131113873 [ ] 0% Error: this SAM file doesn't appear to be correctly sorted! current hit is at chr1:162968481, last one was at chr9:108470655 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.
Code:
@HD VN:1.0 SO:unsorted @SQ SN:chr1 LN:197195432 @SQ SN:chr2 LN:181748087 @SQ SN:chr3 LN:159599783 @SQ SN:chr4 LN:155630120 @SQ SN:chr5 LN:152537259 @SQ SN:chr6 LN:149517037 @SQ SN:chr7 LN:152524553 @SQ SN:chr8 LN:131738871 @SQ SN:chr9 LN:124076172 @SQ SN:chr10 LN:129993255 @SQ SN:chr11 LN:121843856 @SQ SN:chr12 LN:121257530 @SQ SN:chr13 LN:120284312 @SQ SN:chr14 LN:125194864 @SQ SN:chr15 LN:103494974 @SQ SN:chr16 LN:98319150 @SQ SN:chr17 LN:95272651 @SQ SN:chr18 LN:90772031 @SQ SN:chr19 LN:61342430 @SQ SN:chrX LN:166650296 @SQ SN:chrY LN:15902555 @SQ SN:chrM LN:16299 @PG ID:Bowtie VN:0.12.7 CL:"bowtie -p 4 --best --strata -m 1 --sam mm9/mm9 -q SRR032476.fastq SRR032476.sam" SRR032476.4 I354_2_FC30605AAXX:2:1:2:1524 length=35 4 * 0 0 ** 0 0 NGAGGTAGTAGGTTGTATAGTTATCGTATTCCGTT !IIIIIIIIIIIIIIIIII9IIIII,III+IB0H$ XM:i:0
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