User: bdeonovic

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bdeonovic180
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2 years, 8 months ago
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Posts by bdeonovic

<prev • 31 results • page 1 of 4 • next >
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Gene/isoform expression distribution
... Gene/isoform expression is known to be heavy tailed (e.g. could be fit well by a power-law distribution). Any good reference I can use to cite this? ...
rna-seq written 2.8 years ago by bdeonovic180
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Extract nucleotide from read at SNP position
... I have read alignments in SAM format, I have read fastqs, I have genome fasta, and I have a VCF file with locations of SNPs. Is there an easy way to pull out the sequenced nucleotide for each read at the SNPs?  I'm not interested in calling SNPs (this is already done, I have my VCF) but I would lik ...
sam snp rna-seq written 4.1 years ago by bdeonovic180 • updated 3.9 years ago by Biostar ♦♦ 20
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Haplotype RNA-seq data
... What software is available for haplotyping transcriptome data (I have RNA-seq data) ...
haplotype rna-seq written 4.1 years ago by bdeonovic180 • updated 3.3 years ago by colindaven1.8k
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BLAT/PSL format coordinate convention for target strand
... It is always confusing to deal with BLAT/PSL format with regards to coordinate conventions. I find the following links helpful: https://www.biostars.org/p/44633/ https://www.biostars.org/p/84686/ http://genome.ucsc.edu/FAQ/FAQformat.html#format2 It is now clear to me that dealing with the query ...
psl alignment blat written 4.3 years ago by bdeonovic180
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Comment: C: Blat Start And End Position Conventions
... I find this post to always be helpful when I am dealing with this strange coordinate system (along with this great answer by Vikas!) ...
written 4.3 years ago by bdeonovic180
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Comment: C: Long read alignment
... One more thing, when I trried the command you suggested ( bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam) I got something along the lines of index not found. ...
written 5.0 years ago by bdeonovic180
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Comment: C: Long read alignment
... Excellent, I see an option for oxford nanopore 2D reads, what if I want to align template and complement reads?  ...
written 5.0 years ago by bdeonovic180
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Long read alignment
... Does anyone have any recommendations for What aligners to use for long reads (e.g. Pac Bio, Oxford nanopore)? Currently I am using gmap, blast, lastz, and blasr (I'm going to try out blat as well).  What particular parameters to use for these aligners to map long reads well. For pac bio long read ...
alignment rna-seq written 5.0 years ago by bdeonovic180 • updated 5.0 years ago by lh331k
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Comment: C: I have peak files for different histone modifications. How can I see them?
... I'm actually doing similar analysis. See the review references I posted on my question: https://www.biostars.org/p/110471/#110482 ...
written 5.2 years ago by bdeonovic180
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Comment: C: Significance of PLINK epistasis p-values
... You should read up on http://en.wikipedia.org/wiki/Multiple_comparisons_problem I would NOT go with the p<0.05 cutoff. Bonferroni correction might be a bit too conservative. Anything significant if you check FDR? If not, you might be out of luck.  ...
written 5.2 years ago by bdeonovic180

Latest awards to bdeonovic

Popular Question 4.0 years ago, created a question with more than 1,000 views. For Automated Snp Lookup Based On Chr And Bp-Position
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Simulating PacBio long reads and generating consensus
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Gwas: Matched Pairs Logistic Regression
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Plink: Creating Dendrograms Of Ibs Clustering Solutions
Student 4.0 years ago, asked a question with at least 3 up-votes. For Long read alignment
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Gwas: Matched Pairs Logistic Regression
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Plink: Creating Dendrograms Of Ibs Clustering Solutions
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Long read alignment

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