Tag: GRCm38

Why are there more lincRNA genes than transcripts in Mus_musculus.GRCm38.100.gtf?

Why are there more lincRNA genes than transcripts in Mus_musculus.GRCm38.100.gtf? 1 Hi All, There are 52446 annotated genes (ENSMUSG IDs) and 142,699 transcripts (ENSMUST IDs) in Mus_musculus.GRCm38.100.gtf. It makes sense that there are WAY more transcripts than genes. My question, however, is – why are there more genes than transcripts…

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Characterization and expression of DNA sequences encoding the growth hormone gene in African Pygmy Mouse (Mus minutoides)

Abstract We determined the nucleotide sequence of the growth hormone (Gh) gene in Mus minutoides, one of the smallest mammals, where was predicted to be distinct in the functional regions between M. minutoides and Mus musculus. To investigate the evolutionary characteristics of Gh in M. minutoides, we constructed a phylogenetic…

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Good or bad idea to annotate with newer genome build?

Good or bad idea to annotate with newer genome build? 0 Hello Biostars Community, If the probe sequences on a mouse methylation beadchip array is based on the (mm10) GRCm38 genome build, would it be a bad idea to annotate the probes with the latest genome build (mm39) GRCm39? I…

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STAR align multiple files

STAR align multiple files 1 Hi everybody, I am doing alignment to 36 PE samples using star. to make it little bit easy task I wrote a bash loop to align them all with the same command. here is my loop: for i in $(ls raw_data); do STAR –genomeDir index.150…

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IOError [errno 2] No such file or directory: ‘-o’

TopHat error: IOError [errno 2] No such file or directory: ‘-o’ 2 Hello everyone. I’m now running tophat in our server. First, I just simply tried “tophat -p 8 -G <gtf_file> <ref_genome> <fa1><fa2>” and it worked. Then I wrote a for loop scripts but It reported error: [2019-04-03 10:49:16] Beginning…

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