User: mollitz

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mollitz40
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Posts by mollitz

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Answer: A: Coordinates for Transcription Start Site (TSS)
... Also there is a published reference annotation data set (refTSS) here: https://www.sciencedirect.com/science/article/pii/S0022283619302530 http://reftss.clst.riken.jp/ ...
written 25 days ago by mollitz40
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Comment: C: How to create alignment of UTR's for use in TargetScan?
... Hey Jon, did you achieve your goal and want to share your experience with us? ...
written 5 months ago by mollitz40
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Comment: C: Hisat2 or Bowtie2 for ChIP-Seq Data?
... "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)." - HISAT2 website (https://ccb.jhu.edu/software/hisat2/index.shtml) ...
written 12 months ago by mollitz40
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Answer: A: Transposable Elements positions in genome (GTF file)
... The Hammel lab provides GTF annotations: > GTF files for gene annotation can be obtained from UCSC RefSeq, > Ensembl, iGenomes or other annotation databases. GTF files for TE > annotations are customly generated from UCSC RepeatMasker or other > annotation database. They contain two cu ...
written 13 months ago by mollitz40
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Tell Canonical Isoform/Trancsript in gencode
... Hey, is there a way to tell which of the transcripts for a given gene corresponds to the canonical isoform in the Gencode dataset? I couldn't find such information anywhere. Best ...
canonical isoform grch37.hg19 gencode hg19 written 2.0 years ago by mollitz40 • updated 2.0 years ago by Emily_Ensembl19k
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[hg19] Reading genes with CCDS
... Hey, I got a bit lost while trying to access gene sequences in the GRCH37. I downloaded CCDS coordinates (I tried datasets from Enseml an NCBI: ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cds/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ccdsGene.txt.gz along with the provid ...
grch37 coordinates ccds hg19 written 2.2 years ago by mollitz40 • updated 2.2 years ago by Satyajeet Khare1.5k

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Transposable Elements positions in genome (GTF file)

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