User: 1106518271

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110651827160
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Posts by 1106518271

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Some problems of creat DESeqDataSetFromMatrix step by DESeq2
... For this step: dds < - DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~condition) I read a lot of examples on the website, but these examples seems for majority cases, here are three parts ...
R rna-seq written 4 months ago by 110651827160 • updated 4 months ago by Vijay Lakhujani4.0k
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Comment: C: bam_sort_core problem when bam files be processed by samtools
... By the way, will this "error" here lead to give wrong result(${filename}.sorted.bam)? ...
written 4 months ago by 110651827160
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Comment: C: bam_sort_core problem when bam files be processed by samtools
... Got it, many thanks! ...
written 5 months ago by 110651827160
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The order of part processions of RNA-Seq data
... From the bam file file.bam (mapping by star) to htseq-count input data: What's the order of the following steps in general? a. sorted file.bam by name to get file.sorted.bam b. index the file.bam or c. index the file.sorted.bam d. get unique mapping reads from ?.bam Thanks in advance! ...
rna-seq written 5 months ago by 110651827160 • updated 5 months ago by WouterDeCoster38k
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bam_sort_core problem when bam files be processed by samtools
... I sorted my RNA-Seq bam files after mapping by star, and here is my key command line in a for cycle bash file: samtools sort $file -o ${filename}.sorted.bam At last, the one error file shows like: [bam_sort_core] merging from 6 files and 1 in-memory blocks... [bam_sort_core] mergin ...
samtools rna-seq written 5 months ago by 110651827160 • updated 4 months ago by linouhao0
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Comment: C: To do two kind of variables to do differential expression analysis
... Thanks! What's more, for id list (my row of matrix), recommend use mRNA id expresion or gene id expression in general? ...
written 8 months ago by 110651827160
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To do two kind of variables to do differential expression analysis
... A toy example: health mouse: tissue a(replication 3), tissue b(replication 9). disease mouse: tissue a(replication 5), tissue b(replication 6). For health_a_1, health_a_2, health_a_3, health_b_1...each do RNA-seq, got their RPKM list I hope to see tissue a has differences in expression bet ...
R next-gen rna-seq written 8 months ago by 110651827160 • updated 6 months ago by Biostar ♦♦ 20
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The problem of atac-seq analysis process steps with macs2
... ![enter image description here][1] Check with this fig, I'm so confused about these 1. I think signal generation step is not belong to macs2, since it is refer to mapping result, mapping let us know generated signal. 1. And peak calling is a function of macs2 but not mark here, actua ...
chip-seq atac-seq written 8 months ago by 110651827160 • updated 8 months ago by Devon Ryan89k
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Comment: C: How can I get the ordered names or new matrix according to cluster result?
... I see, so kind of you, truly inspirational! ...
written 9 months ago by 110651827160
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Comment: C: How can I get the ordered names or new matrix according to cluster result?
... I seeked this command a long time, thanks! ...
written 9 months ago by 110651827160

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