User: jon.brate

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jon.brate190
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Posts by jon.brate

<prev • 74 results • page 1 of 8 • next >
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... Ok, I'll check it out. Thanks for the advice :) ...
written 6 months ago by jon.brate190
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... Ok, so `-validatePairs` seems to only print out a warning if there are singletons in any of the files? Did both commands give the same output? ...
written 6 months ago by jon.brate190
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... Yes, I can do the trimming and everything and it spits out the two correct paired files and the two single files. But in this case I wondered whether I could use trimmomatic just for filtering out singletons, without doing any trimming or filtering. ...
written 6 months ago by jon.brate190
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... My questions is really how to use trimmomatic with this option? I can't find any mention of it in the manual. I tried to launch trimmomatic with `-validatePairs input1.fq input2.fq paired1out.fq single1out.fq paired2out.fq single2out.fq` but nothing happened. Only the usage menu showed. ...
written 6 months ago by jon.brate190
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... Yes, it's certainly not a job! Thanks! :-) ...
written 6 months ago by jon.brate190
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What is Trimmomatic -validatePairs, and how to use it?
... Hi, I use Trimmomatic v0.35 and I notice the option `-validatePairs`: Usage: PE [-threads ] [-phred33|-phred64] [-trimlog ] [-quiet] [-validatePairs] [-basein | ] [-baseout | ] ... or: SE [-threads ] [-phred33|-phred64] [-trimlog ] [-quiet] ... But I can't ...
trimmomatic written 6 months ago by jon.brate190 • updated 6 months ago by h.mon21k
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Comment: C: Bowtie2 mapping did not finish, can I still use the .sam file?
... Thanks. My interest was more general as I could always redo the mapping properly later. But in this case I'm going to use the mapping in Pilon to polish an assembly. I'm thinking to filter out only properly mapped pairs, and then I will assume nothing is wrong with the .bam file? (if nothing crashes ...
written 8 months ago by jon.brate190
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Bowtie2 mapping did not finish, can I still use the .sam file?
... I mapped a set of paired reads using Bowtie2 but the job was cancelled before it finished. I don't need all the reads mapped for my purposes, so I wonder if I can still use the .sam file or if there are some steps performed at the very end of the mapping which affects the entire file? I am convertin ...
bowtie2 bowtie written 8 months ago by jon.brate190 • updated 8 months ago by WouterDeCoster35k
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Comment: C: BAM file comparison
... I'm looking to do something similar, but instead comparing bam-files of the same input reads mapped to different assemblies to see the fraction of reads mapping to all assemblies. I was thinking to pull out the names of all mapped reads from each bam-file and then maybe simply make a venn-diagram of ...
written 8 months ago by jon.brate190
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Comment: C: MaSuRCA failed to extract the best long reads
... Thanks for your suggestions. I'm also running Canu in parallel so I will see once it' finished. ...
written 9 months ago by jon.brate190

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