User: brown.annaleigh

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Posts by brown.annaleigh

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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 5 weeks ago by brown.annaleigh10 • updated 5 weeks ago by genomax89k
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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 5 weeks ago by brown.annaleigh10 • updated 5 weeks ago by Alex Reynolds30k
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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 6 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 7 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 7 months ago by brown.annaleigh10 • updated 7 months ago by ATpoint38k

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