User: kamiljaron

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kamiljaron70
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Posts by kamiljaron

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... And [BioMake][1] is off the game? It uses prolog (which is both the weakness and the strength...). [1]: https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx306/3806980/BioMake-a-GNU-Make-compatible-utility-for?redirectedFrom=fulltext ...
written 6 days ago by kamiljaron70
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Comment: C: Big Genome Assembly of Medicinal Plant
... 1. How do you know your genome size? 2. Have you tried to estimate a genome size from reads? (for example using https://github.com/gmarcais/Jellyfish). ...
written 5 months ago by kamiljaron70
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Comment: C: How to specify Illumina Single End data in the MaSuRCA Assembler config file
... This have not worked for me (version 11152016). Also, believe that two numbers after tag of the library are not avg/std_dev _read_length but average/std dev fragment length (i.e. the distance of the pair end reads). ...
written 7 months ago by kamiljaron70
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Comment: C: unpaired R1 and R2 sequences
... I am not sure If I understand correctly. Do you mean by "designations in the identifiers" just read IDs? If yes, then the fact that they are unpaired means that there will be always only read with unique ID in the concatenated file, therefore from the perspective of the software there can not be a d ...
written 9 months ago by kamiljaron70
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unpaired R1 and R2 sequences
... Hello, trimomatic reports unpaired R1 R2 after trimming pair-end reads (for those pairs where one of reads failed for some reason). Well, I kind of can not figure out, why it trimmomatic saves unpoired R1 and R2 separately. Is there any particular reason why not to concatenate those two files in on ...
trimmomatic trimming pair-end written 9 months ago by kamiljaron70 • updated 9 months ago by Brian Bushnell12k
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Comment: C: Population-wise decay of linkage disequilibrium (LD)
... It is not too helpful. Anyway, if you have some identification of populations in your file (lets say that CHR_A), than you can just use `subset` function `ld <- read.table("plink.ld",header=T)` `ld$a <- (ld$BP_B-ld$BP_A) #I recomed to use meaningful names, not "a"` `for(family in levels(ld$CH ...
written 15 months ago by kamiljaron70
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Comment: C: Population-wise decay of linkage disequilibrium (LD)
... May be you can solve it on the level of R... How does the plink.ld file looks like? ...
written 15 months ago by kamiljaron70
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Comment: C: pair-end, mate-pairs coding
... I found that this merged fastq files are called interleaved FASTQ (found at webpage of another trimmer [adapterremoval][1]). Using this, I ve googled a [bash script][2] which is probably solution for my problem, but not really answering a question - How it is coded. Is it just the order of sequences ...
written 15 months ago by kamiljaron70
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pair-end, mate-pairs coding
... Hello, recently I received quite big dataset of three pair-end libraries (350, 550, 700 is) and two mate-pairs libraries (Nextera, 3000 and 5000 is). I ve started with [Trimmomatic][1] creating really nicely trimmed pair-ended libs. This procedure failed badly for mate-pairs libraries, due to princ ...
sequence assembly next-gen sequencing written 15 months ago by kamiljaron70
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Comment: C: Pacbio Quiver Consensus - How To Use?
... In documentation of quiver they say that aligned reads should be on input in .cmp.h5 or .bam format... Aligned reads to what, I had some troubles to run pbalign. What do you think, would it be possible to use different mapper?? ...
written 15 months ago by kamiljaron70

Latest awards to kamiljaron

Appreciated 5 months ago, created a post with more than 5 votes. For C: Blast - Formatting Output
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Blast - Formatting Output

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