User: lkianmehr
lkianmehr • 0
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Posts by lkianmehr
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... 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
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written 25 days ago by
lkianmehr • 0
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... 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 ...
written 28 days ago by
lkianmehr • 0
• updated 28 days ago by
Michael Love ♦ 20k
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... 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
lkianmehr • 0
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... 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
lkianmehr • 0
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... 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?
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written 6 weeks ago by
lkianmehr • 0
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... can we do collapseReplicates for each cases, do not have any exclusion?
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written 6 weeks ago by
lkianmehr • 0
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... 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 ...
written 6 weeks ago by
lkianmehr • 0
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... 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 ...
written 6 weeks ago by
lkianmehr • 0
• updated 6 weeks ago by
Michael Love ♦ 20k
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... 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 ...
written 3 months ago by
lkianmehr • 0
• updated 3 months ago by
Michael Love ♦ 20k
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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
lkianmehr • 0
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