User: lkianmehr

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lkianmehr0
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Posts by lkianmehr

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quantifying piRNA and tRNA by Salmon
... Hello,   I have quantified piRNA and tRNA of RNA-seq by Salmon on fasta file, now to do DGE analysis may I use numreads ? what should I do because it is impossible to import them in tximport     thanks in advance ...
dge salmon written 25 days ago by lkianmehr0
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How tximport summerize transcript-level abundance to gene-level
... Hello, Excuse me, I have encounterd with one question about tximport. I have used tximport to import trancript-level abundance from Salmon to gene-level. now I want to choose some of significant genes for confirmation by RT-PCR. but I am not sure may I choose the gene or it's transcript. because ea ...
tximport written 28 days ago by lkianmehr0 • updated 28 days ago by Michael Love20k
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Comment: C: plot of normalized counts for a single gene
... Right, if I assign Dnmt2_1ND and Dnmt2_2ND as two biological replicates, may I use DESeq to make a compare with Dnmt2_1NF and Dnmt2_2NF together? and for another samples which I had, I did DESeq2. I had D1, D3, R1 and R3. each of them has two replicates, D1_L001 and D1_L002 and same this for others ...
written 6 weeks ago by lkianmehr0
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Comment: C: plot of normalized counts for a single gene
... about that case, I have 8 samples, " Dnmt2_1ND", "Dnmt2_1NF", "Dnmt2_2ND", "Dnmt2_2NF", "Dnmt2_3HD", "Dnmt2_3HF", "Dnmt2_4HD", "Dnmt2_4HF ND ,NF , HD and HF have same condition, but they are not tecnical replicates, actuelly their sample has been taken from two different mouse but with the same co ...
written 6 weeks ago by lkianmehr0
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Comment: C: plot of normalized counts for a single gene
... Excuse me, I realised that they are not technical replicates, they have same condition but from two separate samples, so I can't do DGE by Deseq2 bacause it needs replicates, what is your suggestion? ...
written 6 weeks ago by lkianmehr0
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Comment: C: plot of normalized counts for a single gene
... can we do collapseReplicates for  each cases, do not have any exclusion? ...
written 6 weeks ago by lkianmehr0
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plot of normalized counts for a single gene
... Hello, I did plotcounts shows normalized counts for a single gene. two groups contains two sample which are not close together  actually they are not replicates indeed, but the same library sequenced on two lanes. so I would appreciate let me know about such cases  how should I do? can I assign the ...
deseq2 written 6 weeks ago by lkianmehr0
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How get genename by tximport
... Hello, I am trying to get gene name as well as geneid and tx id, but I do not know how. tx2gene.gencode.M19 GRCm38.p6.csv is list of GENEID and TXID. the list of gene and transcript name is in another file like tx2gene.csv could you please guide how can I do it? tx2gene <- read_csv(file.path(d ...
tximport genename written 6 weeks ago by lkianmehr0 • updated 6 weeks ago by Michael Love20k
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Problem with writing CollapseReplicates command
... Hello, I think have problem with writing this command, could you please explain where went wrong exactly with collapseReplicates command? thanks in advance   gr <- factor(c(rep("Dnmt2_ND", 2), rep("Dnmt2_NF", 2), rep("Dnmt2_HD", 2), rep("Dnmt2_HF", 2))) colData <- data.frame(group=gr, typ ...
deseq2 written 3 months ago by lkianmehr0 • updated 3 months ago by Michael Love20k
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Comment: C: how do compare with DESeq2
... data points (samples) are projected onto 3D plane. most of smples of 4 groups concentrate together and on  PC1 axis, samples of 1 of groups has been separated from each other. ...
written 3 months ago by lkianmehr0

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