User: A

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Posts by A

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Comment: C: Quality checking by biological replicates
... They're replicates. So we took from the same pooled RNA So it wouldnt be tumour heterogeneity, but technical variations Does this mean I should average them Thank you ...
written 18 days ago by A3.9k
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Comment: C: Quality checking by biological replicates
... Thank you so much @Kevin Blighe Sorry in the main plate layout, for some samples (Wells) I have duplicates How do I deal with the duplicates here? Do I average them first? Do I pick the first replicate? Do I use both replicates? (If I do the last one won’t it bias the results towards the samples t ...
written 18 days ago by A3.9k
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Quality checking by biological replicates
... HI I have two data setes, in which some samples are from the same patients (library preparation has not been performed at the same time), and some samples are not from the same patients but we have 4 cell lines definitely from the sample patients in two plates (higlighted in yellow) This is the sa ...
R rna-seq written 20 days ago by A3.9k
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Comment: C: Knowing the number of exons in a range
... No I alreadyy run the code and obtained the file like uc001aaa.3 chr1 + 11873 12227 uc001aaa.3 chr1 + 12612 12721 uc001aaa.3 chr1 + 13220 14409 uc010nxr.1 chr1 + 11873 12227 uc010nxr.1 chr1 + 12645 12697 uc010nxr.1 chr1 + 13220 14409 uc010nxq.1 chr1 + 11873 12227 uc0 ...
written 29 days ago by A3.9k
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Comment: C: Knowing the number of exons in a range
... Does this code give me human exons cooradinates? curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c |\ awk '{n=int($8); split($9,S,/,/);split($10,E,/,/); for(i=1;i<=n;++i) {printf("%s,%s,%s,%s,%s\n",$1,$2,$3,S[i],E[i]);} }' ...
written 29 days ago by A3.9k
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Comment: C: Knowing the number of exons in a range
... I need the number of exones in in each range ...
written 29 days ago by A3.9k
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Knowing the number of exons in a range
... Hi I have copy number segment from exome seq like > head(CN) # A tibble: 6 x 6 file Chromosome Start End Total_CN Minor_CN 1 sample1 51479 817980 2 0 How I know how many exones are in the r ...
exome R written 29 days ago by A3.9k
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Answer: A: Manipulating a fasta file to only have specificcharacters
... wget http://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/chromosomes/chr2.fa.gz zgrep -v ">chr" chr2.fa.gz | tr -d '\n' | sed -e '$a\' > chr2.fa ...
written 5 weeks ago by A3.9k
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Comment: C: Creating an interaction network in R
... Thank you my data is in maf. I have two groups so that I want to create two plot with same order of genes but when I put my genes in order argument in maftools that returns an error so I am trying to create the interaction network myself ...
written 5 weeks ago by A3.9k
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Creating an interaction network in R
... Hello I want to create an interaction network of mutations in terms of mutual exclusivity and co-occurance I have this data > dput(dat[1:5,]) structure(list(gene1 = c("XIRP2", "ABCA13", "VIRMA", "AHNAK2", "TPTE"), gene2 = c("CFAP54", "FAT3", "TENM4", "TP53", "CCDC168" ), pVal ...
R written 5 weeks ago by A3.9k

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