User: brown.annaleigh

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Posts by brown.annaleigh

<prev • 6 results • page 1 of 1 • next >
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Answer: A: What packages/tools are available to use SJ.out.tab file obtained from STAR
... Hi there, You can check this out. https://github.com/dzhang32/dasper/ But most tools I believe are developed to work with the aligned data, the BAM files that STAR produced, and then you can hunt through the splice junctions afterwards when you know more what you're looking for. ...
written 7 weeks ago by brown.annaleigh10
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Answer: A: Extract exact match from bed files
... bedtools intersect -f 1 -wa -r -a target.aggregated.bed -b regions_of_interest.bed ...
written 3 months ago by brown.annaleigh10 • updated 3 months ago by GenoMax92k
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Extract exact match from bed files
... I would like to extract only regions which exactly match another bed So I have a regions of interest bed which defines regions, I want to extract only exact matches to these regions cat regions_of_interest.bed chr8 79611214 79636802 annotated 0 - chr8 79611214 79616823 abnormal 0 - Tr ...
bedtools bed bedops written 3 months ago by brown.annaleigh10 • updated 3 months ago by Alex Reynolds31k
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Answer: A: Using Gencode transcript annotation in Kallisto / Sleuth pipeline
... Was googling around for the same question, found an answer on the Kallisto/Sleuth google users group. Their solution was to remove the extra information from the hd5 files https://groups.google.com/forum/#!searchin/kallisto-and-applications/gencode%7Csort:date/kallisto-and-applications/KQ8782UD35E/ ...
written 9 months ago by brown.annaleigh10
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Comment: C: Interested in RNA-Seq splicing analysis - go for paired-end shorter or single-en
... This answers my question perfectly. Thank you! ...
written 10 months ago by brown.annaleigh10
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Interested in RNA-Seq splicing analysis - go for paired-end shorter or single-end longer?
... If I'm about to send something off to sequencing, and my main question is about splicing, am I better off with 75 bp pair-end reads or 150 bp single end? I understand that paired-end is better than single end, and longer is better than shorter, but if I'm weighting between the two, which should I p ...
splicing rna-seq sequencing written 10 months ago by brown.annaleigh10 • updated 10 months ago by ATpoint42k

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