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incompatibility with Cufflinks #4

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
If you set outSAMattributes as All then the sam file generated is incompatible 
with Cufflinks.  The error is something like no XS tag for a spliced read. But 
when one uses outSAMattributes in standard mode and pass the sam file to 
cufflinks then no error is thrown. i think too many new tags when using the All 
mode create confusion for Cufflinks.

Also, i would appreciate if you could add a command line option to add RG, LB, 
SM, PL tags in the SAM file. 

What version of the product are you using? On what operating system?
Latest released version 2.3.0.1 on Linux 

Please provide any additional information below.

Original issue reported on code.google.com by ashutosh...@gmail.com on 15 Apr 2013 at 5:42

GoogleCodeExporter commented 9 years ago 
when you specify  --outSAMattributes All option, STAR outputs extra attributes 
that follow some novel SAM specifications. These attributes are only supported 
by the latest versions of samtools, 0.1.18 and 0.1.19, and will also cause 
problems with some downstream analysis software such as bedTools, HTseq and 
Cufflinks, because, I believe, these software do not use the latest samtools 
API.

I do not recommend using this option unless you really need these attributes. 
You can also cut the columns with these attributes before feeding the 
alignments to other software.

I will add the @RG tags in the next STAR release.

For a quicker reply, please post your questions at 
https://groups.google.com/forum/#!forum/rna-star

Original comment by adobin@gmail.com on 17 Apr 2013 at 9:22