User: ioannis

gravatar for ioannis
ioannis30
Reputation:
30
Status:
New User
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Last seen:
2 months ago
Joined:
1 year, 9 months ago
Email:
i*********************@nord.no

I am a PhD student in Norway and I am working on epigenetics of fish domestication.
Previously I was working mainly with population genetics and microsatellites.
Currently, I am trying to improve my knowledge in bioinformatics and NGS data analysis.

Posts by ioannis

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Finding the number of aligned nucleotides per read in a sam file
... Sorry for taking some time to answer but I am trying to understand how everything works without knowing java basics. The script you shared is working perfectly. Thanks Pierre ...
written 3 months ago by ioannis30
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Comment: C: Finding the number of aligned nucleotides per read in a sam file
... I see, but maybe I didn't make it clear. In the Sequence column I do not get any "-" or any other symbols but I get some aligned reads with chromosome and position that do not much the genomic sequence by one nucleotide. Example: Genomic sequence: AGTCTAGTACCC Aligned sequence: AGCTAGTACCC ...
written 3 months ago by ioannis30
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Finding the number of aligned nucleotides per read in a sam file
... Hi, I have tried a "home-made" method in order to extract the number of nucleotides per read out of a SAM file but is not working correctly for all the reads due to some deletions (I guess). grep -e "pattern" my.sam | cut -f 2,3,4,5 > output.txt To explain, I search for reads with a patter ...
cigar stings sam written 3 months ago by ioannis30 • updated 3 months ago by Pierre Lindenbaum116k
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Comment: C: Count number of characters in every row of a column
... Yes exactly. Thanks a lot Friederike! ...
written 8 months ago by ioannis30
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Comment: C: Count number of characters in every row of a column
... Yes I will import my files into R using read.table(..., stringsAsFactors=FALSE) this will do the job. Thanks a lot Ram. ...
written 8 months ago by ioannis30
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Count number of characters in every row of a column
... Hi community, I was wondering if anyone can give any advice on this: > Chr = c("NC1", "NC2", "NC3") > Pos = c(150, 165, 190) > Seq = c("GATCGATGAC", "GATG", "ACGTAG") > df = data.frame(Chr, Pos, Seq) > df Chr Pos Seq 1 NC1 150 GATCGATGAC 2 ...
R written 8 months ago by ioannis30 • updated 8 months ago by RamRS20k
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Comment: C: Finding motifs across a genome
... It runs like a dream! Thanks a lot Bastien! Cheers, Ioannis ...
written 9 months ago by ioannis30
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Finding motifs across a genome
... Hi community, I would like to find the genomic coordinates of all the CCGG motifs across my reference genome. The only thought to go around this would be to `grep` for CCGG across my reference genome and export these sequences in a fasta format. Then align to the same genome and get the coordinates ...
genome ccgg written 9 months ago by ioannis30 • updated 9 months ago by Bastien Hervé2.8k
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Comment: C: NA values of count matrix in class DESeqDataSet
... > rse_gene <- data.frame(c(1,2,3,4,5), c(1,2,3,4,5), c(1,NA,3,4,5), c(NA,NA,NA,4,5), c(1,2,3,4,5)) > colnames(rse_gene) <- c("a","b","c","d","e") > rse_gene[(is.na(rse_gene))] <- 0 > rse_gene a b c d e 1 1 1 1 0 1 2 2 2 0 0 2 3 3 3 3 0 3 4 4 ...
written 15 months ago by ioannis30
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Model matrix for limma voom
... Hello community, I have a large data set called "DWsub". It looks like this: > head(DWsub, n=3) CDx CWx D53x D63x D66x D68x D70x D72x W53x W63x W66x W68x W70x W72x NC_013663.1-295 10 6 125 699 73 48 69 3 307 29 13 33 5 34 ...
limma model.matrix written 15 months ago by ioannis30 • updated 15 months ago by andrew.j.skelton735.5k

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