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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
