User: diltsjeri

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diltsjeri420
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Posts by diltsjeri

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Comment: C: convert vcf file from GRCh38 to GRCh37 using picard LiftoverVcf
... I'm also getting the same error, but I'm not quite making it to the ' LiftoverVcf Lifting variants over and sorting' step. (java-jdk/1.8.0_92, picard/2.8.1) My vcf doesn't have chr prefixes and I removed the 'chr' in the reference. java -Xmx1G -jar ${PICARD} LiftoverVcf I=./17.2057_passed ...
written 15 months ago by diltsjeri420
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Comment: C: Can I use a gpu to demultiplex with bcl2fastq?
... Yeah the [documentation][1] says cpus only with threading options. [1]: https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2_guide_15051736_v2.pdf ...
written 16 months ago by diltsjeri420
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Can I use a gpu to demultiplex with bcl2fastq?
... Hi, Just brainstorming ways to speed up our pipeline. Demultiplexing is definitely a time hog. I'm not too familiar with exactly how demultiplexing works computationally. Is bcl2fastq written in such a way that it could utilize our gpus? I'm not finding much documentation on the subject. ...
illumina gpu bcl2fastq demultiplex written 16 months ago by diltsjeri420 • updated 16 months ago by Devon Ryan85k
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Comment: C: How can I tell my fastq is a fastqsanger or not?
... Also, for clarification. Is it safe to assume that all the latest nexgen (NexSeq, HiSeq, IonTorrent, etc) technologies are outputting fastqsanger as the .fastq? Or should I just never assume anything? ...
written 21 months ago by diltsjeri420
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Comment: C: How can I tell my fastq is a fastqsanger or not?
... Thanks! Your google skills are better than mine. ...
written 21 months ago by diltsjeri420
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How can I tell my fastq is a fastqsanger or not?
... Hi, If I'm given a fastq file. How am I able to tell if it's a fastqsanger format or not? Is there a command line tool available for this? I really don't want to have to go into galaxy to ensure its format. Thanks! ...
fastq fastqsanger written 21 months ago by diltsjeri420 • updated 21 months ago by genomax57k
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Difference between the original Green Genes db and Green Genes Second Genome?
... Hi! We've been looking at Greens Genes as a potential 16S database. Initially we downloaded the file current_GREENGENES_gg16S_unaligned.fasta.gz from [here][1] (2011), but then we realized there was a second more recent Green Genes [site][2] and downloaded gg_13_5.fasta.gz (2013). What is the cri ...
green genes 16s written 2.5 years ago by diltsjeri420 • updated 2.3 years ago by Biostar ♦♦ 20
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Answer: A: Max fasta file size for creating a udb with Usearch 32-bit? or how to calculate
... ~400MB worked for us. ...
written 2.5 years ago by diltsjeri420
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Max fasta file size for creating a udb with Usearch 32-bit? or how to calculate it?
... What is the maximum fasta file size allowed for creating a udb with USEARCH 32-bit? Or how can we calculate it? So far we have tried a 1.3GB fasta file, but it's too large and we run out of memory (though we have 1008GB of RAM)....I think the developer purposefully limits the processing? We are ...
usearch written 2.5 years ago by diltsjeri420
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Comment: C: Is a fully assembled 129S1/SvlmJ mouse strain available for download? If so wher
... Yeah, that was dumb. I clicked around a bunch and initially couldn't find it. Thanks! ...
written 2.9 years ago by diltsjeri420

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