User: ad

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ad30
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30
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New User
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United States
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2 years, 2 months ago
Joined:
4 years, 9 months ago
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a*****@ucr.edu

Posts by ad

<prev • 21 results • page 1 of 3 • next >
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Comment: C: DNA input for HMMER
... My goal is to find sequences related to group A. I know group A are related through binding assays although it might not be apparent in sequence. I can't just discard sequences until I get a good msa because that would lose information and lead to bias ...
written 2.2 years ago by ad30
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DNA input for HMMER
... Hello, I have a bunch of DNA sequences (group A) I'm going to turn into a Stockholm MSA and I hope to use this to search another collection DNA sequences with nhmmer in HMMER to hopefully pick out anything that might be related to group A. Problem 1: I was reading through the userfile and its not ...
genome alignment sequence written 2.2 years ago by ad30
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Comment: C: Feature/Motif Extraction from Sequences?
... I have a set of CHIPpeaks. I want to extract the sequences and then use some of them to predict other sequences. the rest of the peaks will be the evaluation set. I'd like two solutions or just one if it can fit both criteria. 1. Something that is at least partially interpretable 2. The best perform ...
written 2.5 years ago by ad30
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Feature/Motif Extraction from Sequences?
... Hello, I’m looking to do feature extraction from sets of sequences with a minimum of assumptions for subsequent downstream comparison with other sets. Like for example given ATGAGGA , TTGGCGTA, for category 1 and GGTTGGTT, CCTTAAT for category 2 determine what category AGGAAGEA is in What are th ...
genome sequence alignment snp gene written 2.5 years ago by ad30 • updated 2.5 years ago by simon.vanheeringen180
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Good Pipeline for ChIPexo
... Hello, I was wondering what was an ideal or the 'standard' pipeline for chipexo. Would something like raw seq results->fastq files->Bowtie for alignment -> GEM for peakcalling be good? Will this provide good 'enduser' data for the experimental scientist or is there another standard processi ...
alignment next-gen sequence chip-seq written 2.8 years ago by ad30 • updated 2.8 years ago by Ming Tang2.6k
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Comment: C: BED alignments not positioned properly in IGV
... Isn't the convention in BED to have base 1 be the start? I've never heard of a position 0 in a nucleotide sequence. ...
written 4.4 years ago by ad30
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BED alignments not positioned properly in IGV
... Hi, I have a problem in IGV. When I load a BED file the coordinates do not seem to be aligning properly with ether the sequence loaded or the ruler at the top of the window. First off for example if the start site is 1 IGV seems to treat it as if the alignment starts at the end of the 1st nucleotid ...
sequencing alignment igv written 4.4 years ago by ad30 • updated 3.0 years ago by Trof0
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Comment: C: Search for multiple Patterns in Sequences
... Doesn't seem to work if the strings in the stringset are different sizes. centralMotifSearch<-DNAStringSet(c("TAATTAAT","ATTAATTA","TAATAT","ATTATA")) pCentralMotifSearch<-PDict(centralMotifSearch) ``` Error in .Call2("ACtree2_build", tb, pp_exclude, base_codes, nodebuf_ptr, : el ...
written 4.4 years ago by ad30 • updated 4 months ago by RamRS26k
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Search for multiple Patterns in Sequences
... Hi, is there a way to use matchPattern from Biostrings to search for a set of patterns rather than just one? If not is there any similar alternative? I'm using it this so far and it doesn't work matchPattern("TAATTAAT|ATTAATTATAATAT|ATTATA",subSeq) and MotifSearch<-DNAStringSet(c("TAATTAAT" ...
sequence bioconductor pattern written 4.4 years ago by ad30 • updated 4.4 years ago by Michael Dondrup47k
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creating BAM? alignment files for IGV
... Hi, I have coordinate data for several sequences I want to align against genomes in IGV. The preferred format for alignment is said to be BAM. Unfortunately I haven't found a straightforward way of creating BAMs straight from coordinates. I assume I'll need the reference genome as well. Is there any ...
genome R alignment myposts written 4.5 years ago by ad30

Latest awards to ad

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Strand Specificity of Arrays and RNAseq
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