Moderator: dariober

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dariober9.0k
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Posts by dariober

<prev • 775 results • page 1 of 78 • next >
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Answer: A: GATK gradlew bundle Error
... I surmise this has nothing to do with GATK but with gradle. Googling `java.security.ProviderException: java.security.InvalidKeyException: EC parameters` leads to this [issue][1] which suggests OpenJDK7 is the culprit. As suggested there, try upgrading to OpenJDK8 in case you are also on 7. This is, ...
written 23 hours ago by dariober9.0k
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Answer: A: bwa mem without -M option how to continue using picard
... Is it still the case that picard (MarkDuplicates?) chokes on split reads? I would check that first. Using `-M` option is a hack to make picard work but it would be better avoiding it since the shorter split of a read is not a "secondary alignment" and there is nothing necessarily wrong with split re ...
written 12 days ago by dariober9.0k
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Comment: C: What are the methods to downsample the Depth of coverage (ex: 50X -> 25X)?
... Out of curiosity, where did you get `readCounter` from? At a glance I don't see it in [HMMcopy][1]. Does your downsampled bam have any reads at all? Try `samtools view -c input_15X.bam` or just `ls -lh input_15X.bam` to see if it has a decent size. [1]: https://bioconductor.org/packages/rel ...
written 13 days ago by dariober9.0k
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Answer: A: Where can I find GV .genome files for igvtools
... Just to demystify the "genome file"... This is just a tab-separated table with one row per chromosome giving chromosome name and size like `chr1 247249719` (I don't remember if the file name has to end with `.chrom.sizes`). So it is quite simple and you could prepare it by yourself. For hg18 I thi ...
written 13 days ago by dariober9.0k
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Answer: A: Overlap of variants between CaVEMan and MuTect2 ?
... Hi- some random thoughts... > the overlap goes to at least 80% I think that depends a lot on the particular sample(s) you are looking at. If you have variants with high frequency than both methods should pick them up. As you go towards lower allele frequencies then the discrepancy inevitably in ...
written 17 days ago by dariober9.0k
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Answer: A: Is there an available tool to visualize multiple "types" of ChIP-seq peaks on a
... If you are looking for an exploratory analysis directly from the command line you could try [ASCIIGenome][1] (I'm the author). Something like: ASCIIGenome gene.bed chipseq1.bed chipseq2.bed ... Would give you something like [this][2] ![enter image description here][3] [1]: http://asciigenome. ...
written 27 days ago by dariober9.0k
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Comment: C: How to get a matrix gene weights in NMF
... Hopefully you get the idea. But on reading again your question make sure that what you need is instead the H matrix of the transpose of the expression matrix. ...
written 28 days ago by dariober9.0k
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Answer: A: How to get a matrix gene weights in NMF
... I think what you want is the W matrix which you can get with the `basis` command (NMF package), E.g.: # A matrix of 20 genes and 10 samples mat<- matrix(runif(n= 200, min= 0, max= 100), nrow= 20, ncol= 10) library(NMF) res<- nmf(mat, rank= 2) w<- basis(res) h&l ...
written 29 days ago by dariober9.0k
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Answer: A: Why IVG coverage track from bam and bigwig files looks different?
... Some wild guess... > bigwig file it seems to I have lots of read in rRNA locus This may be due to some rescaling when converting bam to bigwig. For example, rescaling to have library size 10M reads will appear as having more reads compared to rescaling to have 1M reads. (Such rescaling can be ...
written 29 days ago by dariober9.0k
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Answer: A: How to generate random genomic sequences that are GC- and length-matched to my i
... Among the many programs that I hacked together, there is [MarkovSequenceGenerator][1] which may be you can make use of. As I remember, just like the OP, I needed a null distribution of sequences matching nucleotides and di-nucleotide content. So this program shuffles sequences in a fasta file using ...
written 4 weeks ago by dariober9.0k

Latest awards to dariober

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 13 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 29 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Scholar 7 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 9 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 3 months ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
Popular Question 6 months ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
Great Question 7 months ago, created a question with more than 5,000 views. For Add read group to header after samtools merge

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