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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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STAR / strandedness not working - missing XS attribute in SAM file #487

Closed paniccodewriter closed 10 years ago

paniccodewriter commented 10 years ago

When running RNAseq analysis using STAR and strandedness, the XS attribute is not set by STAR (missing from --outSAMattributes NH HI NM MD AS). This leads to cufflink errors: BAM record error: found spliced alignment without XS attribute.

Star cmd line: .../STAR --genomeDir.../genomes/Rnorvegicus/rn5/star --readFilesIn .../xxx.fastq --runThreadN 22 --outFileNamePrefix .../xxx --outReadsUnmapped Fastx --outFilterMultimapNmax 10 --outSAMunmapped Within --outSAMattributes NH HI NM MD AS --outSAMattrRGline ID:12 PL:illumina PU:xxx SM:xxx

roryk commented 10 years ago

Hi Magnus,

Thanks a lot for the bug report. For stranded data STAR doesn't set the XS tag on purpose, section 8.2.3 of the manual explains why, it is a little confusing:

http://rnastar.googlecode.com/files/STARmanual_2.3.0.1.pdf

The Cufflinks that runs in bcbio-nextgen was not setting --library-type flag as described in the manual with stranded data and that is why Cufflinks was failing. I think 8f24fa4 should fix it.