User: bharata1803

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bharata1803430
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Japan
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2 months, 2 weeks ago
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4 years, 10 months ago
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Posts by bharata1803

<prev • 239 results • page 1 of 24 • next >
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Comment: C: Salmon tximport get TPM
... I see. Thank you for your feedback. I will use rlog or VST because I usually use that. I totally forget about it and just think maybe I can use TPM directly. ...
written 11 weeks ago by bharata1803430
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Salmon tximport get TPM
... Hello, In Salmon result, there is a TPM column but it is from transcript level. I want to use tximport library to get TPM values for gene level. per_gene <- tximport(salmon_file_list, type = "salmon", tx2gene = trs2gene) I use that code and I get this: names(per_gene) [1] "abunda ...
salmon rna-seq written 11 weeks ago by bharata1803430
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Comment: C: Extracting important gene with similar expression level from multiple samples
... I am familiar with WGCNA, which function that you refer? I only know WGCNA for building network from coexpression network. My cohort now is about 5 datasets. Each datasets has more than 3 ipsc samples. So, I think it is quite enough. One of them also come from different ceell type. Most of them are ...
written 12 weeks ago by bharata1803430
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Extracting important gene with similar expression level from multiple samples
... Hello all, So, after collecting several samples of iPSC (RNA-seq) data from independent NCBI GEO dataset, I think not all iPSC has similar gene expression profile. I also read from paper that gene expression of iPSC may varied. In that case, I collect 4-5 iPSC samples from multiple NCBI GEO datase ...
feature extraction rna-seq clustering written 3 months ago by bharata1803430 • updated 3 months ago by piyushjo170
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Comment: C: Finding similarities of 2 independent samples
... Well, same in the definition of gene expression. What I imagine is if I clustered the sample, I will be able to group them in the same category. I understand this will be affected by sample normalization or sequencing variance. Is there any method to normalized this variance? ...
written 4 months ago by bharata1803430
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Finding similarities of 2 independent samples
... Hello, So, I downloaded from 2 NCBI GEO dataset with same type, iPSC. Is it possible to compare whether these 2 samples of iPSC are the same or not? My goal is to find whether reprogrammed cell from same mature cell (fibroblast) produce same iPSC. What kind of method is possible? Thank you. ...
rna-seq written 4 months ago by bharata1803430 • updated 12 weeks ago by Biostar ♦♦ 20
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Fastq-dump error time exhausted
... I had received this error while batch downloading via fastq-dump. fastq-dump.2.8.2 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) The problem is, it seems all fastq downloaded. There are no ...
ncbi fastq rna-seq written 6 months ago by bharata1803430
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DE genes effect in regulatory network for time course data
... Hello, I am asking a bit general question here about analysing time course data. If you ever deal with time course data, maybe you can share your experience because it is my first time. So, is there any tools to analyse change in gene expression that are happening in a time course data? My goal is ...
grn deseq2 rna-seq written 6 months ago by bharata1803430
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Answer: A: DEG from BAM file
... To do DEG analysis, what you need is a readcount table. So, you just need read count software that accept BAM files. Try HTSeq count or featureCount. After you get read count table, you can do DEG using popular library like DESeq2, EdgeR, or limma/voom. ...
written 8 months ago by bharata1803430
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Differential expression analysis for time course data
... Hello, I want to ask regarding time course data. The data I want to analyse is from human iPSC cell reprogramming with time course data from mature cell induce with Yamanaka factor to become iPSC with several time steps. What are the best ways to do this? Firstly, I am thinking to use CPM as a me ...
deseq2 rna-seq written 8 months ago by bharata1803430

Latest awards to bharata1803

Popular Question 4 months ago, created a question with more than 1,000 views. For Samview from bam file aligned to cDNA reference
Popular Question 4 months ago, created a question with more than 1,000 views. For Samview from bam file aligned to cDNA reference
Popular Question 4 months ago, created a question with more than 1,000 views. For Samview from bam file aligned to cDNA reference
Popular Question 6 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 8 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 9 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 10 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 11 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Student 11 months ago, asked a question with at least 3 up-votes. For Download human 3 UTR FASTA file
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Couldn't able to run the DESeq2
Scholar 12 months ago, created an answer that has been accepted. For A: How to visualize a set of sequence alignments that all have the same reference s
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Dataset kind of data NCBI
Popular Question 14 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 14 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 14 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 14 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file

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