Re: [Samtools-help] Picard release 1.46

[mei ge <rge...@ya...>]

Hi Alec:
 
I used your ribosomal interval file and I got an error as follow:
 
[Thu May 26 13:50:45 EDT 2011] net.sf.picard.analysis.CollectRnaSeqMetrics REF_FLAT=/home/gtf/hg19/refFlat_table_for_picard.txt RIBOSOMAL_INTERVALS=/home/gtf/ribosomal_RNA/Homo_sapiens_assembly19.rRNA.interval_list STRAND_SPECIFICITY=NONE 
INPUT=/s_1_2_pefca_2/s_1_2_pefca_2_sorted.bam OUTPUT=/s_1_2_pefca_2/s_1_2_pefca_2_RNAseq_metrics.txt REFERENCE_SEQUENCE=/databases/hs_chromosomes/hg19.fa ASSUME_SORTED=true 
VALIDATION_STRINGENCY=SILENT 
STOP_AFTER=0 
VERBOSITY=INFO 
QUIET=false 
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
INFO 2011-05-26 13:50:46 CollectRnaSeqMetrics Loaded 21987 genes.
[Thu May 26 13:50:46 EDT 2011] net.sf.picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=165347328
Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (25, 85)
at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:84)
at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:126)
at net.sf.picard.analysis.CollectRnaSeqMetrics.setup(CollectRnaSeqMetrics.java:86)
at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:101)
at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
at net.sf.picard.analysis.CollectRnaSeqMetrics.main(CollectRnaSeqMetrics.java:77)


--- On Thu, 5/26/11, Alec Wysoker <al...@br...> wrote:


From: Alec Wysoker <al...@br...>
Subject: Re: [Samtools-help] Picard release 1.46
To: "mei ge" <rge...@ya...>
Cc: "Sam...@li..." <Sam...@li...>
Date: Thursday, May 26, 2011, 10:58 AM


Hi Robin,

Human HG19 is attached.  I don't have one for mouse.  I just extracted these from gencode GTF file.  Presumably you could do the same for mouse. Interval list format described here: http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html

Note that this file is not required by CollectRnaSeqMetrics, but if you do not provide it the program will not be able to determine when reads map to rRNA.

-Alec

On 5/26/11 9:54 AM, mei ge wrote: 





Hi Alec:
 
I am looking for human (hg19) and mouse(mm9).
 
Thanks
Robin

--- On Wed, 5/25/11, Alec Wysoker <al...@br...> wrote:


From: Alec Wysoker <al...@br...>
Subject: Re: [Samtools-help] Picard release 1.46
To: "mei ge" <rge...@ya...>
Cc: "samtools help" <sam...@li...>
Date: Wednesday, May 25, 2011, 4:52 PM


Hi Mei,

Are you looking for human?  If so, what genome build?

-Alec

On 5/25/11 3:15 PM, mei ge wrote: 





Hi Alec,
 
I use the CollectRnaSeqMetrics in the new release Picard.  I don't know where to get the Ribosomal_intervals file.  Can you point a place for the file?
 
Thanks
Mei