User: Merlin

gravatar for Merlin
Merlin 10
Reputation:
10
Status:
New User
Location:
Italy
Last seen:
2 days, 9 hours ago
Joined:
11 months, 3 weeks ago
Email:
p********@operapadrepio.it

Posts by Merlin

<prev • 27 results • page 1 of 3 • next >
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DESeq and checkFullRank(modelMatrix)
... Hello guys, I am running DESeq2 to compare 4 different conditions and I have a problem with a commmand line. dds = DESeqDataSetFromMatrix(countData = countMatrix, colData = coldata, design = ~ group + treatment +group:treatment) although I found online many others people solved the same prob ...
deseq2 rna written 2 days ago by Merlin 10 • updated 2 days ago by Michael Love23k
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DESeq2 statistic and design
... Hello everyone, I am using DESeq2 for DEG analysis. I have a set of experiment which consists of 4 duplicates and it's not clear how to create the design object? Here is my condition: condition<- factor(c (group1 =rep ("treatment1",time=2), group2 = rep("treatment2",time=2), group3= rep(" ...
deseq2 rna written 8 days ago by Merlin 10 • updated 8 days ago by Michael Love23k
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DESeq2 LFCshring=2 or 4
... Hello Everyone, I am using DESeq2 for DEG analysis. I have a total of 8 samples( 1 duplicate for each condition so 4 different conditions) At this point of the analysis: resultsNames(dds) resLFC <- lfcShrink(dds, coef=4, res=res, type="apeglm") I know that this part is used for shinkin ...
deseq2 written 10 days ago by Merlin 10 • updated 10 days ago by Michael Love23k
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Comment: C: quant.sf files and tximport, transcripts not recognized
... Thank you for you answer Michael, Yes It’s at least three days that I m checking my work, and I have also tried to put the two messages indicated in the output but it didn’t work because I ddin’t use the complete command =TRUE. Slowly I’m learning everything I’m sorry for taking your time, if you ...
written 19 days ago by Merlin 10
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Comment: C: quant.sf files and tximport, transcripts not recognized
... I'm not sure if it's read_tsv that is wrong since I don't have tsv file or there is something more required and related to summarizeToGene function it says this as well, None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that ...
written 20 days ago by Merlin 10
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quant.sf files and tximport, transcripts not recognized
... Hello Folks, I generated quant.sf file with Salmon tool and the next step is to Import the transcripts abundance dataset with tximport. I generated the file.csv using the same annotation file used in salmon, > head(tx2gene) TXNAME GENEID 1 ENST00000456328 ...
salmon tximport written 20 days ago by Merlin 10 • updated 20 days ago by Michael Love23k
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Comment: C: Salmon (quant.sf) to tximport error
... Ok I fixed the problem, I modified the codes, mainly by writing the entire paths for all the codes and fixing the variable file.path. all(file.exists(files)) >[1] TRUE ...
written 24 days ago by Merlin 10
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Comment: C: Convert BAM to FASTQ
... Hi ioannis.vardaxis, I never done this in R environment but I can assure that is very easy using samtools in unix. this is the code: samtools fastq input.bam > output.fastq if your BAM is a paired end you have to split the fastq generated cat output.fastq | grep '^@.*/1$' -A 3 --no- ...
written 24 days ago by Merlin 10
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Comment: C: Salmon (quant.sf) to tximport error
... Ok Michael, I will follow your suggestion Thanks ...
written 24 days ago by Merlin 10
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Comment: C: Salmon (quant.sf) to tximport error
... To be honest with you I though that $run was a function of R, I learned something more, thanks. I did some adjustment, I have different results but still the same error... files <- file.path("salmon", samples$condition, "~RNAseq/salmon_folder/salmonSFquant/treated_1/quant.sf", ...
written 24 days ago by Merlin 10

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