User: 14134125465346445

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Posts by 14134125465346445

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Comment: C: Affy 500K positions in hg38
... Has anybody produced a bed file for the 23andme/Illumina/Affy rsIDs on hg38? ...
written 16 months ago by 141341254653464453.4k
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Comment: C: How to update a 23andme, vcf or plink bed file to hg38?
... Has anybody produced a bed file for the 23andme rsIDs on hg38? ...
written 16 months ago by 141341254653464453.4k
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Comment: C: Calling SNPs with low coverage
... BBmap must have changed since this answer was provided. Do you know what's the updated command-line for this in BBMap_36.28.tar.gz? ...
written 16 months ago by 141341254653464453.4k
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Calling differential peaks on large set of 3 conditions
... Hi all, What are the recommended methods to call differential peaks for enrichment/pulldown datasets (e.g. MEDIPS, H3K4me3) of different conditions with many replicates? - 20-30 biological replicates of condition1 pulldown+input pairs - 20-30 biological replicates of condition2 pulldown+input pair ...
peak calling differential macs2 written 21 months ago by 141341254653464453.4k
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Comment: C: bam file calculate sliding window insert sizes
... That would be great! ...
written 22 months ago by 141341254653464453.4k
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648
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bam file calculate sliding window insert sizes
... Hi all, I have a bam file with paired-end reads of relatively uneven coverage, and I want to produce a wiggle plot with the sliding window of insert sizes. Is there a tool for this? ...
insert size bam written 22 months ago by 141341254653464453.4k • updated 22 months ago by Devon Ryan88k
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bam stats F1F2/F1R2/R1F2/R1R2/F2F1/F2R1/R2F1/R2R1
... Hi, I would like to know the statistics of the different read pair orientations for a bam file aligned with bwa mem. I tried bamtools stats, but it does not split the counts into all possible orientations: F1F2/F1R2/R1F2/R1R2/F2F1/F2R1/R2F1/R2R1 Is there a piece of software that will give me the ...
bam written 23 months ago by 141341254653464453.4k • updated 23 months ago by John12k
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Picard MarkDuplicates stuck at Traversing read pair information and detecting duplicates
... Hi, I am running Picard MarkDuplicates on a mid-size bam of about 5GB. The process starts as expected, but after about half an hour, it gets stuck at 'Traversing read pair information and detecting duplicates.'. I left the process to run for about 16 hours, and it didn't complete. I rekicked it, a ...
picard markduplicates bam written 2.0 years ago by 141341254653464453.4k
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non-metric multidimensional scaling for RNAseq or enrichment experiments
... After reading this paper: http://journal.frontiersin.org/article/10.3389/fgene.2016.00191/full I would like to know what are the pros/cons of using non-metric multidimensional scaling for RNAseq or other enrichment experiments: https://en.wikipedia.org/wiki/Multidimensional_scaling#Non-metric_mul ...
enrichment rna-seq written 2.1 years ago by 141341254653464453.4k
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IGV idxsession files with bigwig URLs
... Hi, Is there a recipe to generate IGV idxsession files with bigwig URLs? I can successfully do it for .bam/.bai pairs, but I wonder if there is an equivalent for .bw files? Is there an index of .bw format? Does IGV support this? ...
bigwig igv written 2.1 years ago by 141341254653464453.4k

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