Activity for floflooo
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floflooo posted a comment on discussion Help
Hi Muhammet, First, thing, the default -abundance_model is uniform, so if your goal is to produce an uniform distribution of all reference sequences, you can omit the -abundance_file parameter. Second, the default -total_reads is 100, so with such as small number, you may not have exactly 10 reads from each of your 10 references, but close to that (since this process is based on probabilities). Hope this helps! Best, Florent
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Hi Laetitia, I finally had the time to have a look at your example. The problem is that you added several sources of errors in your command. Specifically, the Balzer homopolymer model is the one that causes the extra indels you observe. Since you want to model Illumina reads anyway, omit any homopolymer model (these models are more suited for 454 reads). And let me re-iterate what I said in a previous email. If you run into issues, you need to find the smallest reproducible example (few reference...
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Hi Guilherme, Grinder is not multi-threaded. However, you can run several Grinder processes simultaneously to take advantage of multiple processing cores. For example, you create a small Bash script that runs 1 Grinder process per chromosome. A note about Grinder speed. There can be a specific performance decrease when you use very large genomes (e.g. human chromosomes) or a very large number of smaller genomes, since all reference sequences are read and kept in memory simultaneously by Grinder....
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Hi Aditi, Grinder was written to simulate sequencing errors, but you could likely indirectly use it to include genomic variant "errors". This is an approach I have not tested: 1/ Input your genomes one by one in Grinder and introduce some errors using the error model desired. For the read length parameter, you will need to provide the exact length of your genome to avoid it being truncated or excluded. 2/ After your variants are ready, concatenate them into a single FASTA/FASTQ file. You may need...
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Mutations when no error model specified
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Hi Chad, Have a look at the description of the reads: 1 reference=test1 position=1..99 2 reference=test1 position=complement(1..99) No errors were introduced. However, as you see, some of the reads were generated from the reference sequence itself and some others from its reverse-complement, as you would expect from random shotgun sequencing. If your use-case calls for unidirectional reads, have a look at the -unidirectional option. Cheers, Florent
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Hi Mao, The Illumina model from Korbel assumes that the reads are 100bp. You will need to adjust the parameters if your reads are longer. I suggest you experiment in Excel with this equation (Korbel et al 2009) to keep the same error rate at the last position as you find for reads that are 100 bp: 3e-3 + 3.3e-8 * i^4 Best, Florent
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Hi Mao, That's an interesting idea, but it is not supported by Grinder. Best, Florent On Wed, Jun 20, 2018, 20:29 Maoxuan Lin mlin18@users.sourceforge.net wrote: Hi Ginder, I am using Grinder to simulate paired-end reads using a set of reference sequences. My goal is to guarantee every reference sequence has been selected to simulate reads. When I increased the total number of reads to large enough, I achieved this goal. However, I could not find a general rule or specific parameters to achieve this;...
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Thank you for confirming this, Ted. As far as I can tell, I have toggled all BIOS settings that seemed relevant. So, I will contact Dell and see if they can patch the BIOS.
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Cannot wake up from suspend using USB mouse/keyboard
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Sorry, the image above is best opened in a new tab: https://medias.audiofanzine.com/images/normal/tuxguitar-1-2-477626.jpg The track displayed in black is the Percussion track.
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Position marker is not visible on tracks that are colored in black
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It works for me in TuxGuitar 1.4 on Linux. The documentation path is then: file:///opt/tuxguitar/share/help/about.html
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Playback of current tab stops when closing a different tab
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Opening the same file again opens in a new tab
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Tabs opened from the TuxGuitar Browser shown as "Untitled.tg"
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Trying again with TuxGuitar 1.4 and it seems to work fine. Cheers and feel free to close this issue.
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Trying again with TuxGuitar 1.4 and it seems to work fine. Cheers!
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Too many repeats in GPX files
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Abundance file bug
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Hi, The sofware is correct. It does not find reference sequence AE000666 because it is not amplified by the primers you provided. You need to not request this sequence or modified your primers so that they amplify it. Best, Florent
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How to generate Illumina amplicon reads with pairwise overlap?
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Use the -id <insert_dist> option. From the manpage: "The insert is defined in the...
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Improved interface for the poly4 error model, i...
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Small internal cleanup
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Ok, good, closing.
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06-seed.t failing test
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Bug in read generation with paired-end and coverage.
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Hi there! Thanks a lot, I did not think about this potential issue before. This is...
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Using Test::Warn to test and silence warnings
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Silenced an expected warning during testing
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Grinder version 0.5.4
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Test update
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Fix for the last mate pair sometimes missing th...
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Moved exec from 'script/' to conventional 'bin/...
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Seems to work fine on my side with perl 5.20.2 Could you try to individually upgrade...
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Error when generating chimeras
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read_dist parsing problem
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Hi Francisco, I have added documentation to clarify what the intended usage is when...
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More dev doc updates
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Added some docs about the dev version
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Fix for Perl 5.18's hash_randomization (reporte...
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Updated test on forbidden chars
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Errors and warnings in linux Ubuntu
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Hi Francisco, Regarding the Statistics::R, R, distrplus warning, I suspect that you...
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Hi Noemi, You need to set the parameter -forward_reverse to produce amplicon datasets...
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Hi Piotr, The problem is that using kmer-based chimeras requires reference sequences...
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Tests failure
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Version 0.4.5
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Fixed bug when parsing arguments with missing v...
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Thanks for checking this harborsiem. This means that the bug report can be close...
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I guess this bug report is invalid, then. Unfortunately, I cannot close it myself....
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StringIndexOutOfBoundsException when opening a GP5 file
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Unable to open GP5 files with UTF8 BOM
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That sounds great! Hopefullly, you can make a release soon? I believe there is initial...
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Trivial code reduction
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More concise test messages
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POD update regarding dependencies
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Consistent indentation
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Revised dependencies... No need to bundle Biope...
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Database test improvements (patch by Francisco ...
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Fix hash randomization in K-mer tests
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Clean temporary DB files
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Sequencing error tests more deterministic (patc...
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Deterministic tests of community structure (rep...
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FASTQ quality value problem
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status: open --> closed
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ArrayIndexOutOfBoundsException when opening a GP5 tab
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