User: benformatics

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benformatics2.0k
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ETH Zurich
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Posts by benformatics

<prev • 227 results • page 1 of 23 • next >
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... > I just misused tools? I think you are confused by **0 vs 1-based coordinate systems**: https://www.biostars.org/p/84686/ If you [liftOver the following site from hg19 to hg38][1] : SNP: rs200923174 - hg19 - chr22:16287557-16287557 becomes - hg38 - chr22:15690406-15690406 [1]: https:/ ...
written 20 days ago by benformatics2.0k
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Answer: A: Calculating GC content around a specific genomic location
... R version: library(Biostrings) library(GenomicFeatures) ## load fasta dna <- readDNAStringSet('your_genome.fasta') ## find your relevant chromosome grep('chr3',names(z.dna),value=T) ## if it is present subset by that chr and rename for convenience dna.chr3 < ...
written 5 weeks ago by benformatics2.0k
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Comment: C: Is ENA API down?
... Yeah similar to the NCBI - but probably a little more frequently - sometimes I'm also unable to connect to the ENA when trying to pull data from the SRA/ERA. ...
written 5 weeks ago by benformatics2.0k
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Comment: C: Get all rows matching to list
... Can you do `head(df)` and include what is shown. It could be that the file isn't importing correctly. Also your write.table command wont work you need to uncomment (i.e. remove ##) from the part of my code. It will then create files named: ab3feea76dbe8d5688328e879961352c.txt 16c306238059e7942361b ...
written 5 weeks ago by benformatics2.0k
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Answer: A: how to get all rows matching to list in R
... ## read your data.frame in df <- read.delim('large_tab_delimited_data_file_like_this.tsv',sep='\t') ## create your list for matching ##your.list <- unique(df$OTU) your.list <- list("OTU1","OTU2","OTU3") ## subset your df object by the OTU values in your lis ...
written 6 weeks ago by benformatics2.0k
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Comment: C: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
... To clarify, **the goal of the shifting is to identify the center of the Tn5 dimer complex binding event.** ...
written 6 weeks ago by benformatics2.0k
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Answer: A: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
... The reason is the Tn5 binds as a dimer and includes a 9 bp spacer in between the two cut sites. **My guess is the decision is arbitrary, you are probably free to shift -4 and +5. Your peaks would still be in the same regions and I don't think anyone is doing single-nt resolution ATAC-seq analysis.* ...
written 6 weeks ago by benformatics2.0k
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... When you say transcripts... what do you mean exactly? After aligning the newly trimmed reads the number of alignments to transcripts is the same. Yes I would say if any trimming occurred it would be very suspicious to see EXACTLY the same number of alignments. If you mean the total number of genes ...
written 11 weeks ago by benformatics2.0k
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Comment: C: Issue installing rmats using conda
... Is this after installing it with conda or downloading the "pre-compiled" version? ...
written 12 weeks ago by benformatics2.0k
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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 3 months ago by benformatics2.0k

Latest awards to benformatics

Scholar 3 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 5 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Appreciated 8 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Scholar 9 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 10 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 13 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 13 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
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
Appreciated 17 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Concept behind p-value correction?
Scholar 17 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 17 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Guru 17 months ago, received more than 100 upvotes.

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