User: kamiljaron

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kamiljaron100
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Posts by kamiljaron

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Kallisto pseudobam to IGV
... Hi, the author is here. I wrote this script for one use only (I was not trying to make a very general resource for everybody, but maybe I should). The problem is that you got differently formatted gtf file and I am using instead of some implemented parsers simply my own. These are lines parsing a g ...
written 9 months ago by kamiljaron100
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Comment: C: Adding Read Groups To Bam Files
... I think this solution is invalid. 1. you need to escape @ character, so it would be at least : `perl -e 'print "\@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illumina\n\@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"' > rg.txt`. The second problem is that the line defined only the header and `-r` flag will assign readgrou ...
written 11 months ago by kamiljaron100
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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 11 months ago by kamiljaron100
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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 16 months ago by kamiljaron100
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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 18 months ago by kamiljaron100
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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 20 months ago by kamiljaron100
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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 20 months ago by kamiljaron100 • updated 20 months ago by Brian Bushnell15k
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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 2.2 years ago by kamiljaron100
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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 2.2 years ago by kamiljaron100
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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 2.2 years ago by kamiljaron100

Latest awards to kamiljaron

Popular Question 29 days ago, created a question with more than 1,000 views. For unpaired R1 and R2 sequences
Appreciated 16 months ago, created a post with more than 5 votes. For C: Blast - Formatting Output
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Blast - Formatting Output

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