User: FGV

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FGV100
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Posts by FGV

<prev • 37 results • page 1 of 4 • next >
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Query UCSC Browser
... Dear all, I'm trying to query the UCSC database directly from the command line (or R) to get the conservation (e.g. phastCons46wayPrimates) score for a single position. I tried using the Table Browser, and it worked fine: track type=wiggle_0 name="Primate Cons" description="Primate Conservati ...
api ucsc written 6 weeks ago by FGV100
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Answer: A: Paired-end and single-end reads combined during RNAseq - acceptable?
... For a de-novo assembly PE reads are actually the most informative and it is usually advisable to have several PE libraries with different insert sizes (e.g. [here][1]) You can combine together PE and SE reads and there are several programs that allow for it (e.g. Velvet). You can also get some mor ...
written 7 weeks ago by FGV100
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Answer: A: Mapping scaffolds to chromosomes
... How big are the genomes? If small you can try MAUVE or MUGSY... I needed to align some bird genomes a while ago, and in the end had to use MULTIZ. It is a bit of a pain to use but it the end it worked. You might also be interested in looking into [minimap2][2] or [cactus][1]. I've never used any o ...
written 7 weeks ago by FGV100
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Answer: A: How can I make GATK fasta alternate reference maker faster
... I'd suggest splitting your analysis by chromosome/scaffold/contig (or a group of them), and running each one of them in parallel. In the end you can just concat all the files. However, be careful with GATK FastaAlternateReferenceMaker, since it will only replace on the reference alternate alleles o ...
written 7 weeks ago by FGV100
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Answer: A: GNU parallel error: Command line too long
... I've been thinking a bit more about this and I think I've found a way around it using `extglob`. Right now I have the commands like: cat /long/path/file1 /long/path/file2 /long/path/file3 /long/path/file4 /long/path/file5 [...] /long/path/file10000 | mafft cat /long/path/file10001 /long/p ...
written 8 weeks ago by FGV100
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Comment: C: GNU parallel error: Command line too long
... Hmmm, I think it is a `parallel` issue (or rather `execve`), since I can run the commands directly on the terminal. From what I understood, parallel uses `execve` to run the commands, and that has a much smaller buffer (apparently 20x smaller) than the terminal limit (seen as `getconf ARG_MAX`). ...
written 3 months ago by FGV100
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Comment: C: GNU parallel error: Command line too long
... But it is exactly the `cat` that breaks the limit because I am doing it on several thousand files. I guess I could do the `cat` directly on the terminal (no `parallel`), and then use `parallel` to run all the alignments since these are the time intensive steps... ...
written 3 months ago by FGV100
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Comment: C: GNU parallel error: Command line too long
... Well, the command is basically a `cat` of several files and then piped into MAFFT. I guess I could split the cat into several `cats`, and pipe it at the end.. but that is a bit error-prone and I'd like to avid it if possible. ...
written 3 months ago by FGV100
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Comment: C: GNU parallel error: Command line too long
... What about making it more optimistic? :) ...
written 3 months ago by FGV100
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Comment: C: GNU parallel error: Command line too long
... It is the list of arguments that is too large. ...
written 3 months ago by FGV100

Latest awards to FGV

Scholar 8 weeks ago, created an answer that has been accepted. For A: GNU parallel error: Command line too long
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Fit Mixture Of Gamma And Negative Binomial Distributions In R
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Implement Bgzip Into C Program
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Samtools Vcf Reference And Alternate Alleles
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Simulate Ngs Mapped Reads

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