From: mei ge <rge...@ya...> - 2011-05-27 18:48:51
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Hi Alec, I need the ribosomal interval file for mouse. Where did you get the gencode gtf file? Thanks Robin --- 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 |