How many transcripts?

How many transcripts are there in common model species reference annotation files?

[17:21] cohenl06@phoenix1 ~ $ cut -f9 /local/data/iGenomes/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf | cut -d ";" -f1 | sort | uniq | wc -l
23366
[17:21] cohenl06@phoenix1 ~ $ cut -f9 /local/data/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf | cut -d ";" -f1 | sort | uniq | wc -l
23368
[17:22] cohenl06@phoenix1 ~ $ cut -f9 /local/data/iGenomes/Drosophila_melanogaster/UCSC/dm3/Annotation/Genes/genes.gtf | cut -d ";" -f1 | sort | uniq | wc -l
15340
[17:22] cohenl06@phoenix1 ~ $ cut -f9 /local/data/iGenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf | cut -d ";" -f1 | sort | uniq | wc -l
40076
[17:22] cohenl06@phoenix1 ~ $ cut -f9 /ifs/home/cohenl06/data/reference/sacCer3_annot.gtf | cut -d ";" -f1 | sort | uniq | wc -l
6692
[17:22] cohenl06@phoenix1 ~ $ cut -f9 /local/data/iGenomes/Arabidopsis_thaliana/NCBI/TAIR10/Annotation/Genes/genes.gtf | cut -d ";" -f1 | sort | uniq | wc -l
26995

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About Lisa Cohen

PhD student at UC Davis.
This entry was posted in Bioinformatics. Bookmark the permalink.

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