User: benformatics

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benformatics2.0k
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ETH Zurich
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Posts by benformatics

<prev • 218 results • page 1 of 22 • next >
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Comment: C: key lookup changes with AnnotationDbi version
... Official response is that the responsibility for lack of these annotations falls on NCBI. The R packages just wrap the publicly available data. https://support.bioconductor.org/p/134782/ ...
written 21 hours ago by benformatics2.0k
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Comment: C: How to identify mRNA 3' UTR by bulk RNA-seq data
... StringTie should still work for the assembly ...
written 22 hours ago by benformatics2.0k
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Answer: A: key lookup changes with AnnotationDbi version
... Based on my limited investigation I'm not quite sure it's `AnnotationDbi` but more likely the version of the `org.Hs.eg.db` package you have installed. I think that the lookups are mainly going through org.Hs.eg.db to find matches through the entrezID. You can also just switch *hgu219.db* with *org. ...
written 3 days ago by benformatics2.0k
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Answer: A: Issue installing rmats using conda
... If your conda is not working specifically for rmats. You could try alternatively creating a Python 3.6 or Python 2.7 environment with conda and then downloading the pre-built package (for your respective python version) from the rmats maintainer: https://github.com/Xinglab/rmats-turbo/releases/tag/ ...
written 4 days ago by benformatics2.0k
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Comment: C: Issue installing rmats using conda
... As of the newest release: http://rnaseq-mats.sourceforge.net/ **It is now:** > Compatible with both Python 2 and Python 3 *As a side note, I'm successfully running rmats v4.1.0 with python v3.6.5 installed through conda in August* ...
written 4 days ago by benformatics2.0k
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Comment: C: Preventing alignment to new Splice Junctions with STAR
... You can read more here: https://groups.google.com/u/1/g/rna-star/c/J6qH9JCysZw/m/VmgoGKSE9qQJ If you want to modify the actual outputs in the splice junction files. ...
written 5 days ago by benformatics2.0k
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Answer: A: Preventing alignment to new Splice Junctions with STAR
... [As per the manual][1]: The parameter: `--alignSJoverhangMin` sets the: **minimum overhang for *unannotated* junctions** Whereas, the parameter: `--alignSJDBoverhangMin` sets the: **minimum overhang for *annotated* junctions** Note the presence of SJDB vs. SJ in the latter, this refers to yo ...
written 5 days ago by benformatics2.0k
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Answer: C: Keep metadata gc column using GenomicRanges
... You cannot keep the metadata in the way you running your command. > ‘range’ returns an object of the same type as ‘x’ containing range > bounds for each distinct (seqname, strand) pairing. The names > (‘names(x)’) and the metadata columns in ‘x’ are dropped. The `range` call will ...
written 6 days ago by benformatics2.0k
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... It is also good to keep in mind the overall alignment parameters you are using. A common artifact that I notice in RNA-seq experiments are coverage spikes. Overtrimming or undertrimming could both contribute to the formation of these artifacts. However, I would agree with ATpoint that it is better ...
written 6 days ago by benformatics2.0k
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Comment: C: bed file indexing problem
... Even though unix sort will probably be faster you could also sort `sample.bed` with [bedtools][1] (default parameters are probably fine) bedtools sort -i sample.bed > sample_sorted.bed [1]: http://%20https://bedtools.readthedocs.io/en/latest/content/tools/sort.html ...
written 11 days ago by benformatics2.0k

Latest awards to benformatics

Scholar 4 days ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 8 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Appreciated 5 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Scholar 6 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 8 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 10 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 11 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 11 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 14 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Concept behind p-value correction?
Scholar 14 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 14 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Guru 14 months ago, received more than 100 upvotes.

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