User: wayj86

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wayj8610
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Posts by wayj86

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Could you please tell me how should I analyze the difference between KO and WT mouse sequenced by 10X genomics?
... Dear all, 10X Single-cell RNA-seq were performed on four mouse samples, two KOs (only one gene was knocked out) and two WTs. KO1 and KO2 have the same weeks of age with WT1 and WT2, respectively. The purpose of this study is to investigate the difference between KO and WT, as well as the impact of ...
rna-seq written 7 months ago by wayj8610
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Comment: C: Which software should be used to calculate the TPM values of genes?
... Yeh. WGCNA usually takes FPKM data, but I was told TPM was much better than FPKM. That is why I need to calculate TPM. ...
written 17 months ago by wayj8610
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Comment: C: Which software should be used to calculate the TPM values of genes?
... Thank you very much for your answer. I need TPM to perform WGCNA, actually. ...
written 17 months ago by wayj8610
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Which software should be used to calculate the TPM values of genes?
... Hi all, I am using STAR to align my reads to human genome. Then I need to calculate the TPM values of genes. There are many software that can be used to do that: Stringtie, RSEM, kallisto, Salmon, salfish, ... So which one is best for doing that? Many thanks, Stanley ...
rna-seq written 17 months ago by wayj8610
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Comment: C: 98.21% of input gene IDs are fail to map
... Copy that. thank you ...
written 17 months ago by wayj8610
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Comment: C: 98.21% of input gene IDs are fail to map
... Dear Uncle Y, thank you very much for your answer. It's my honor to meet you here. I am your big fan: ) ...
written 17 months ago by wayj8610
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98.21% of input gene IDs are fail to map
... Hi all, I am using clusterProfiler to perform KEGG enrichment. I have a list of gene Symbol (Rat genes). First I need to translate the symbols to EntrezID. I installed the Genome wide annotation for Rat: source("https://bioconductor.org/biocLite.R") biocLite("org.Rn.eg.db") Then I tried ...
R clusterprofiler written 17 months ago by wayj8610 • updated 17 months ago by Mike Smith1.2k
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Comment: C: Incompatibility between the output of STAR and RSEM
... Thanks. I have marked my post up. This is the my first time to post a topic in Biostars: ) ...
written 18 months ago by wayj8610
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Incompatibility between the output of STAR and RSEM
... Hi all, I aligned my data with STAR, and then calculated the expression with RSEM: STAR --runMode alignReads --runThreadN 2 --genomeDir ~/ref_ensemble_ERCC/star_ref/ --readFilesIn ~/WJC-RNAseq/WJC-3/WJC-3_clean_r1.fq ~/WJC-RNAseq/WJC-3/WJC-3_clean_r2.fq --quantMode TranscriptomeSAM GeneCount ...
rna-seq written 18 months ago by wayj8610 • updated 18 months ago by WouterDeCoster40k

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Popular Question 3 months ago, created a question with more than 1,000 views. For Which software should be used to calculate the TPM values of genes?
Popular Question 5 months ago, created a question with more than 1,000 views. For 98.21% of input gene IDs are fail to map

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