MM9

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Hiroshi Yamamoto’s MM9 | Skulls in the Stars

Search Forums. Go to Page RefseqGene vs Ensembl for mm9. Hello, I would like to ask for your opinion regarding a reference transcriptome for mm9.

My task is to search for "novel" transcripts in RNA-seq data aligned to mm9, so I am wondering what would be my best option to use as reference? From both tracks I created gtf files with the genePredToGtf tool.

Index of /CEAS/src/mm9

Suprisingly for me the ancient Ensembl release was much more comprehensive than its up to date RefseqGene counterpart: Ensembl67 vs. RefseqGene Quote:. Location: Freiburg, Germany. Is there a reason you're using mm9 still?


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It's fairly unsurprising that old Ensembl releases contain more transcripts than current refseq releases. The former is more comprehensive by design, with refseq typically only containing very well annotated isoforms. Originally Posted by dpryan.

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It's just a function of when you start work compared with time since last release in the build cycle. Also, it has been a while since mm10 is out so its the right time to make the transition. And for other annotations you can always liftOver mm9 to mm Log In.

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Welcome to Biostar! Please log in to add an answer. I have got raw count of mouse RNA reads. Thank you so much in advance. My question is how can I use data provided from dbSNP to remove ger I need to reanalyze certain dataset rna seq paired end stranded, bp that has been already ana I am build indexing structure for mouse mm9 genome with the following command: rsem-prepare-ref Hi all, I am new to chip-seq analysis.

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I am using Bowtie to align one fastQ file to reference ge I need centromeric location for mouse mm Tried using data from ucsc gap tables but the infor