User: benformatics

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benformatics490
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Posts by benformatics

<prev • 51 results • page 1 of 6 • next >
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Answer: A: Identify adapter sequences for trimming from Illumina paired end fastq files
... [fastp][1] is a new tool that is almost as fast as `bbduk` but has implemented methods that **automatically** detect 5' or 3' adapters for both paired (must be manually enabled) and single-end data. > the adapters are evaluated by analyzing the tails of first ~1M reads So if you have more compl ...
written 3 days ago by benformatics490
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Answer: A: MACS2 option for ATAC seq?
... The [official Harvard guidelines][1] as of this year suggest the following: > Our previous recommendation was to run MACS2 with -f BAMPE, which is > similar to the default analysis mode of Genrich (inferring full > fragments, rather than cut site intervals). Others have attempted to > i ...
written 3 days ago by benformatics490
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Comment: C: MS level RESEARCH IDEA
... Or at least it is not one of the purposes of this specific forum ...
written 3 days ago by benformatics490
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Comment: A: MACS2 option for ATAC seq?
... Please try using the search function as the answers to your question have been presented in the past: https://www.biostars.org/p/209592/ ...
written 3 days ago by benformatics490
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Answer: A: How to get number of exons for each transcript in biomart
... Or use R with a transcript database (you can make your own from any GTF using the *makeTxDbFromGFF* command from the *GenomicFeatures* library): ## setup transcriptDb txdb <- TxDb.Mmusculus.UCSC.mm10.ensGene ## get exon locations for each gene exons <- exonsBy(txdb,'gene') ...
written 4 days ago by benformatics490
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Comment: C: shall we consider -- keep-dup all when we removed duplication?
... Yes that would be true but hopefully when he/says that says they remove them and mentions samtools flags AND picard. My sincerest hope is that they flagged the duplicates with samtools and removed with MarkDuplicates (parameter: REMOVE_DUPLICATES=true) ...
written 4 days ago by benformatics490
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Answer: A: shall we consider -- keep-dup all when we removed duplication?
... Unless you merged different libraries in a downstream step (post-duplicate removal) or alternative deduplicated using UMIs (or something similar) then **it shouldn't matter because you should no longer have duplicate reads in your samples**. Feel free to try both with and without; the results shoul ...
written 4 days ago by benformatics490
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Answer: A: Differential Expression and Co-expression analysis from Cell type-specific datas
... The thing is that just because those genes **aren't being actively translated** (i.e. present in your TRAP data) doesn't mean they aren't present/transcribed at biologically significant levels in the cells. TRAP sounds like an enrichment method of known targets so it make sense to use the *true neg ...
written 5 days ago by benformatics490
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Comment: C: Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... What do you mean by "parsing all lines in R as a vector to filter, as I already wrote a filter that gives index positions."... You can pretty easily convert all the VCF information to data.frames but getting it back into VCF format is not as easy. What exactly do you want to extract? and what is yo ...
written 5 days ago by benformatics490
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Answer: A: Error in as.vector(x) : no method for coercing this S4 class to a vector
... You can't cbind a bunch of obscure object types. If you want merged count tables you should do this: mdat <- do.call(cbind,lapply(dat,assay)) Where *row.names* are **Ensembl gene IDs** and *col.names* are the **SRR accessions**. Then run your `write.table(mdat, "recount_mdat.csv")` comman ...
written 5 days ago by benformatics490

Latest awards to benformatics

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 11 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Scholar 5 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
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: ATAC-seq peak calling with MACS
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Scholar 17 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 18 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS

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