User: jon.brate

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jon.brate200
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Norway
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Posts by jon.brate

<prev • 78 results • page 1 of 8 • next >
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Comment: C: Trying to get access to the Trinity R commands...
... Thanks, I began installing a local copy of Trinity (on my Macbook), but I had problems compiling it so I stopped. Any experience installing Trinity locally? ...
written 25 days ago by jon.brate200
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Comment: C: Trying to get access to the Trinity R commands...
... Thanks, I found those, but I was actually looking for the R commands which are generated with the different perl scripts under the Differential Genexpression (I think a file called RScript is generated after running the perl script). These are no magic commands, but I am just interested in learning ...
written 25 days ago by jon.brate200
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Trying to get access to the Trinity R commands...
... On the server I use it is not so easy to install the necessary R packages when using `R --vanilla`, so I can't run the Trinity perl scripts which uses R for differential gene expression and visualizations (basically everything described [here](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trin ...
trinity rna-seq R written 25 days ago by jon.brate200
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Comment: C: Error Runnin miRDeep2
... Sorry for the late answer, I am not sure I understand your problem. My error was about the reference genome, not the miRNAs. And I am not sure which 'b' character you refer to, the one in the miRNA name? ...
written 25 days ago by jon.brate200
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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 8 months ago by jon.brate200
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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 8 months ago by jon.brate200
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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 8 months ago by jon.brate200
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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 8 months ago by jon.brate200
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... Yes, it's certainly not a job! Thanks! :-) ...
written 8 months ago by jon.brate200
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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 8 months ago by jon.brate200 • updated 8 months ago by h.mon23k

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Great Question 7 months ago, created a question with more than 5,000 views. For How to extract the longest isoform from multi fasta file
Student 7 months ago, asked a question with at least 3 up-votes. For Plot statistics from gtf/gff file
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Popular Question 15 months ago, created a question with more than 1,000 views. For How to get different colors on coverage tracks in IGV
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to extract the longest isoform from multi fasta file
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Plot statistics from gtf/gff file
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Popular Question 3.6 years ago, created a question with more than 1,000 views. For Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Extract gene sequences from gff3 file and reference fasta

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