User: mollitz

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mollitz60
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Posts by mollitz

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Comment: C: Is It Possible To Get Fragment Length, Read Length And Number Of Fragments From
... To underline what @Carlo Yague pointed out. This answer does *not* represent what most people refer to the term "insert size". See here: https://www.biostars.org/p/95803/ This forum lacks a down-vote button (similar to stackexchange) ...
written 3 months ago by mollitz60
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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 11 months ago by mollitz60
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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 15 months ago by mollitz60
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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 23 months ago by mollitz60
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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 23 months ago by mollitz60
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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 2.9 years ago by mollitz60 • updated 2.9 years ago by Emily_Ensembl21k
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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 3.0 years ago by mollitz60 • updated 3.0 years ago by Satyajeet Khare1.6k

Latest awards to mollitz

Appreciated 4 months ago, created a post with more than 5 votes. For A: Transposable Elements positions in genome (GTF file)
Popular Question 10 months ago, created a question with more than 1,000 views. For [hg19] Reading genes with CCDS
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Transposable Elements positions in genome (GTF file)

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