Question: Problem With Running Cufflinks
0
Yan He • 240 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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modified 6.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
6.3 years ago by
Yan He • 240
