User: bharata1803

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bharata1803420
Reputation:
420
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Japan
Last seen:
2 weeks, 6 days ago
Joined:
4 years, 6 months ago
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Posts by bharata1803

<prev • 235 results • page 1 of 24 • next >
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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 21 days ago by bharata1803420
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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 25 days ago by bharata1803420
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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 9 weeks ago by bharata1803420
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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 9 weeks ago by bharata1803420
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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 4 months ago by bharata1803420
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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 4 months ago by bharata1803420
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Comment: C: Getting raw FASTQ file from GDC/TCGA database
... well, I need the raw data because I want to use transcript level gene expression for my method. Unfortunately, GDC only has gene level expression result. So, I think having raw data myself, I could get the transcript level expression by myself. Currently I use data from NCBI GEO because there are m ...
written 5 months ago by bharata1803420
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Getting raw FASTQ file from GDC/TCGA database
... Hello, I just want to know whether we can obtain raw data from GDC/TCGA database. I heard they require you to submit some request but I don't know how to do it. I am a student so my credentials is very limited. Maybe I can ask my Professor to submit it if needed. Also does it takes long time for th ...
next-gen rna-seq written 5 months ago by bharata1803420 • updated 4 months ago by Biostar ♦♦ 20
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FIMO parameter for PWM motif scanning
... Hello, I have several questions regarding the use of FIMO as motif scanning. I have used it for a while but I still don't understand some part of it. 1. Regarding low complexity region or repeating region. I noticed that FIMO result actually match a lot with repeating region. Does this mean anythi ...
fimo pwm written 6 months ago by bharata1803420
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Comment: C: Subread and featurecounts read index and annotation once for all
... Usually I use salmon, but this time the fastq is colorspace. So, I need to use aligner that support colorspace which is subread. I am used to use salmon with fast process and now stuck in subread with 30 minutes per file processing. ...
written 7 months ago by bharata1803420

Latest awards to bharata1803

Popular Question 21 days ago, created a question with more than 1,000 views. For Samview from bam file aligned to cDNA reference
Popular Question 25 days ago, created a question with more than 1,000 views. For Samview from bam file aligned to cDNA reference
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 4 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 5 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 6 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 7 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Student 7 months ago, asked a question with at least 3 up-votes. For Download human 3 UTR FASTA file
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Couldn't able to run the DESeq2
Scholar 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Dataset kind of data NCBI
Popular Question 10 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 10 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 10 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 10 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 12 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file

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