Admin: Hervé Pagès

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Hervé Pagès ♦♦ 11k
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Posts by Hervé Pagès

<prev • 1,367 results • page 1 of 137 • next >
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Answer: A: A bug of "seqlevels<-" on TxDb
... Hi Can Wang, Thanks for the report. This should be addressed in GenomicFeatures 1.26.1 (release) and 1.27.5 (devel). Unfortunately there is another issue at the moment in GenomicFeatures that breaks makeTxDbFromBiomart() and will prevent the updated GenomicFeatures from propagating to the public re ...
written 5 weeks ago by Hervé Pagès ♦♦ 11k
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Comment: C: findSpliceOverlaps Buffer Error
... findCompatibleOverlaps() is only about detecting aligned reads that are compatible with the splicing of the transcript that they overlap. findSpliceOverlaps() does a little bit more: it also tells you whether the read is compatible with only one annotated transcript. The Overlap Encodings vignette ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Answer: A: matching of AAStringSet vs. another AAStringSet
... I'm not aware of the notion of iterator in R in general. If you only have 10-20k queries, you can simply use a for loop. The overhead of looping over an AAStringSet object of length 20k is not much, only 6 sec on my machine: library(Biostrings) library(hgu95av2probe) peptides <- translate(DNAS ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Comment: C: how to make findOverlaps from genomicAlignments package to consider soft-clipped
... Oops, not so fast! Sorry I forgot that cigarRangesAlongReferenceSpace() reports a zero-width range for the S in the CIGAR: > cigarRangesAlongReferenceSpace("2S47M3I24M3S", with.ops=TRUE)[[1]] IRanges object with 5 ranges and 0 metadata columns: start end width <integer& ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Answer: A: how to make findOverlaps from genomicAlignments package to consider soft-clipped
... Hi, If we agree that it wouldn't make sense to have the interval in-between read pairs account in the overlap calculation without also having the so called "skipped regions" (i.e. N in the cigars), then you can completely ignore the fine range structure of each pair and replace it by a single range ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Answer: A: matching of AAStringSet vs. another AAStringSet
... Hi Tobi, You have only 1 peptide so why use matchPDict/vmatchPDict? Functions in the matchPDict family are meant to be used on a set of short motifs. If you only have 1 motif, use functions from the matchPattern family instead. More precisely, if you have 1 sequence in your subject, use matchPatter ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Answer: A: Return features from a single strand using vmatchPattern
... Hi, Note that TCAG is not a palindrome: > motif <- DNAString("TCAG") > reverseComplement(motif) 4-letter "DNAString" instance seq: CTGA   Anyway, to answer your question: no, vmatchPattern() doesn't have an option for searching only one strand of the genome. Filtering out the matches ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Comment: C: findSpliceOverlaps Buffer Error
... Thanks for sending me the dataset privately (35929048 paired-end reads). With this dataset findSpliceOverlaps() took about 2h to complete and used more than 200 Gb of RAM on a Linux server at Fred Hutch. It returned a Hits object with 144261871 annotated hits between the reads and the transcripts. I ...
written 6 weeks ago by Hervé Pagès ♦♦ 11k
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Comment: C: Memory-efficient method to calculate GC content of millions of GRanges
... Hi, Creating the BSgenomeViews object doesn't load anything from disk. And displaying it only loads the content of the views that are being displayed. Note that the above implementation of letterFrequency2 loads the content of 500000 views at a time. You can change this by modifying the value of c ...
written 7 weeks ago by Hervé Pagès ♦♦ 11k
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Comment: C: findSpliceOverlaps Buffer Error
... Sorry but I can't use this code to reproduce the problem. I don't have the gencode.v25.annotation.gff3 file on my computer and you're not telling us where you got it from. Also I don't know what bamFilePath is. In other words, it's not standalone code. Standalone code is code other people can copy/p ...
written 8 weeks ago by Hervé Pagès ♦♦ 11k

Latest awards to Hervé Pagès

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Scholar 10 months ago, created an answer that has been accepted. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Scholar 10 months ago, created an answer that has been accepted. For A: calculate frequency of non-overlapping matches for a motif in a XStringSet
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: annotatePeak() in ChIPseeker - how long does it take to run?
Scholar 10 months ago, created an answer that has been accepted. For A: calculate frequency of non-overlapping matches for a motif in a XStringSet
Scholar 11 months ago, created an answer that has been accepted. For A: calculate frequency of non-overlapping matches for a motif in a XStringSet
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Appreciated 11 months ago, created a post with more than 5 votes. For A: GenomicAlignments: Inverting strand when counting using summarizeOverlaps
Scholar 11 months ago, created an answer that has been accepted. For A: calculate frequency of non-overlapping matches for a motif in a XStringSet
Scholar 11 months ago, created an answer that has been accepted. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Scholar 12 months ago, created an answer that has been accepted. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Scholar 12 months ago, created an answer that has been accepted. For A: getting a directed and unweighted adjacency matrix with igraph package
Scholar 12 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 12 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Scholar 14 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 14 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Scholar 14 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Scholar 14 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 14 months ago, created an answer that has been accepted. For A: a package for read.fasta
Scholar 14 months ago, created an answer that has been accepted. For A: a package for read.fasta

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