User: yueli7

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yueli7140
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Posts by yueli7

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Comment: C: integrate eight single cell *.csv files into one *.csv file
... Hello Mensur Dlakic, Thank yo so much for your great help! You are right! Best, Yue ...
written 6 weeks ago by yueli7140
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principal component analysis (PCA) of single cell samples which come from different libraries
... Hello, I have 17 single cell samples which come from different libraries. They are 8 healthy, 3 mild and 6 severe patients samples. First, I want to do the principal component analysis (PCA) of these 17 samples to see whether the healthy samples can cluster together. Which package I can use? T ...
rna-seq written 6 weeks ago by yueli7140 • updated 6 weeks ago by ATpoint36k
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Comment: C: integrate eight single cell *.csv files into one *.csv file
... Hello ATpoint, Thank you so much for your response! I downloaded the files from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122960. These files ended with: *_filtered_gene_bc_matrices_h5.h5. I used cellranger mat2csv to transfer eight files into csv format. Right now, I want to merg ...
written 7 weeks ago by yueli7140
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integrate eight single cell *.csv files into one *.csv file
... Hello, I have eight single cell *.csv files and want to integrate them into one *.csv file Then I can do the downstream Seurat analysis: https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html. How can I do it? Thanks in advance for great help! Best, Yue ...
rna-seq written 7 weeks ago by yueli7140 • updated 7 weeks ago by Mensur Dlakic5.8k
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Comment: C: which gtf file I can use?
... Hello, ATpoint, Thank your so much for your quick response and detailed explanation! Thank you and Best! Yue ...
written 7 weeks ago by yueli7140
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which gtf file I can use?
... Hello, I use star to make human index. I have hg38.fa file which downloaded from: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ There are four gtf files:`hg38.refGene.gtf.gz, hg38.ncbiRefSeq.gtf.gz, hg38.knownGene.gtf.gz and hg38.ensGene.gtf.gz `in: http://hgdownload.soe.ucsc.edu/golden ...
rna-seq written 7 weeks ago by yueli7140
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Comment: C: How can I use Seurat with *_filtered_gene_bc_matrices_h5.h5 files
... Hello, MatthewP, Thank you so much for your great help! Best, Yue ...
written 7 weeks ago by yueli7140
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How can I use Seurat with *_filtered_gene_bc_matrices_h5.h5 files
... Hello, I only have the single cell with `*_filtered_gene_bc_matrices_h5.h5` format. 1. I have eight samples, and want to combine them together. 2. I want to use Seurat to do the downstream analysis. How can I do? Thanks in advance for any help! Best, Yue ...
rna-seq written 8 weeks ago by yueli7140 • updated 8 weeks ago by MatthewP660
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Comment: C: what is the mean of the file "*._f1.fq.gz" and "*._r2.fa.gz"
... Hello, Mensur Dlakic, Thank you so much for your response! You are correct! These two files are paired-end files. They have the same headers. Thank you again! Best, Yue ...
written 8 weeks ago by yueli7140
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what is the mean of the file "*._f1.fq.gz" and "*._r2.fa.gz"
... Hello, I downloaded the files from: https://bigd.big.ac.cn/gsa/ The file is ended with: " *._f1.fq.gz" and " *._r2.fa.gz". 1. Is it single-end or paired-end sequencing? 2. If it is paired-end sequencing, the file should be: " *._r1.fq.gz" and " *._r2.fa.gz", not " *._f1.fq.gz". Thanks in adv ...
rna-seq written 8 weeks ago by yueli7140 • updated 8 weeks ago by Mensur Dlakic5.8k

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