User: olikidrod

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olikidrod0
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Posts by olikidrod

<prev • 7 results • page 1 of 1 • next >
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Lifting over macaque microarray data from one species reference (hg19) to another (macaque)
... I used an Illumina iScan microarray, designed for humans and based on hg19, to genotype macaques. Based on prior advice in Biostars, I was able to export from Illumina's proprietary IDAT format into PLINK, and then export into VCF. Thus, I now have a VCF based on hg19. Recently, we sequenced a bunc ...
vcf iscan picard microarray liftover written 5 months ago by olikidrod0
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Comment: C: Might @PG headers affect downstream analyses, and how can I safely remove them f
... Many thanks for your quick reply. Yes; I checked, Picard did not add one. I'll strip out the @PG lines to avoid confusing anyone later. ...
written 6 months ago by olikidrod0
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Might @PG headers affect downstream analyses, and how can I safely remove them from a BAM file?
... I've been mapping BAM files with bwa, and had bwa add read groups during the mapping. As a consequence, the exact command that I used to execute bwa is thus included in the @PG headers in all the BAM files. That obviously includes the read groups specified. Since then, I've used Picard to replace a ...
read groups bam @pg written 6 months ago by olikidrod0 • updated 6 months ago by h.mon27k
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Comment: C: Best approach for parallelizing bwa mem over multiple CPUs
... Thanks for this. My understanding is that -t only refers to number of threads, whereas I need to parallelize over multiple physical servers and CPUs. Thus, I decided to go with brute-forcing as suggested in '3.' For anyone else who stumbles across this, I chose to used bbmap to verify that paired F ...
written 7 months ago by olikidrod0
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Best approach for parallelizing bwa mem over multiple CPUs
... I would like to parallelize bwa mem on multiple cores across multiple CPUs, on our high-performance computing cluster. This was previously discussed seven years ago in this thread: https://www.biostars.org/p/16191/. With that in mind, I'm now considering that the best way to do this is either: 1) U ...
hpc parallel bwa written 7 months ago by olikidrod0 • updated 7 months ago by genomax71k
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Comment: C: Map bed file probes against genome
... Brilliant -- thank you! ...
written 14 months ago by olikidrod0
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Map bed file probes against genome
... I have a .bed file containing probes for a commercial microarray and would like to map these against a reference genome in NCBI, for which the probes were not originally designed. I'd like to see how many map with near perfect identity; if it's the majority, we'd go ahead and use it. Can anyone sugg ...
alignment written 14 months ago by olikidrod0 • updated 14 months ago by h.mon27k

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