User: bharata1803

gravatar for bharata1803
bharata1803360
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360
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Japan
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3 hours ago
Joined:
3 years, 10 months ago
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b**********@gmail.com

Posts by bharata1803

<prev • 209 results • page 1 of 21 • next >
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Answer: A: Dataset kind of data NCBI
... The annotation come from the microarray platform. You should check the platform information first every time you download public data because it may come from different platforms. I believe that there is an R library which can decode the gene annotation for each microarray platform but you can also ...
written 3 hours ago by bharata1803360
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Comment: C: Couldn't able to run the DESeq2
... You can try another library in R called tximport. https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html The link above is a full tutorial how to import data to DESeq2. It also includes data from StringTie. Maybe it can solve your problem quicker. ...
written 4 hours ago by bharata1803360
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Filtering low count when using Tximport from Salmon to DESeq2
... Hello, So I've used salmon to extract readcount and use tximport to be used in DESeq2. After I perform DE analysis, there are some genes that has NA result. I suspects that this is caused by low count or maybe even 0 readcount result. Should I filter the low count gene before performing DE analysis ...
deseq2 rna-seq written 1 day ago by bharata1803360 • updated 1 day ago by h.mon21k
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Comment: C: Transcript differential exprs analysis using Kallisto not significant
... Yes aI am thinking to use DESeq2 and combine it with Salmon/Kallisto readcount result. ...
written 6 days ago by bharata1803360
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Comment: C: Transcript differential exprs analysis using Kallisto not significant
... well generally I know why transcript has low power. i want to find a way to handle this problem. the reason why i am interested is related to transcription factor. I what TF regulates are not gene but transcript and transcript also translate into protein. I cannot go into detail here because to be ...
written 7 days ago by bharata1803360
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Comment: C: Transcript differential exprs analysis using Kallisto not significant
... Yes, that is correct.To be precise, I want to investigate which transcript cause the up/down regulation of the gene expression in disease compare to control. I am thinking the logFC of transcript diff. exprs. analysis would be a weight of how a transcript expression affect overall gene expression. ...
written 7 days ago by bharata1803360
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Transcript differential exprs analysis using Kallisto not significant
... Hello, So I performed both gene level and transcript level expression analysis. I have 7 samples (matching) of normal and cancer. For gene level analysis, I use Salmon to both (pseudo)align and quantify readcount. I then use DESeq2 library from Bioconductor. For gene level analysis, I follow Kalli ...
rna-seq written 7 days ago by bharata1803360 • updated 7 days ago by kristoffer.vittingseerup780
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Kallisto estimated sd and fragment length
... Hello, I want to ask about the significance of sd and fragment length for Kallisto. Will Kallisto prduce totally different result if the parameter is different? I use from public data and it mention like this: "RNA-seq was performed using Illumina HiSeq 2500 System with 100 nucleotide single-end re ...
alignment kallisto rna-seq written 16 days ago by bharata1803360
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Comment: C: Finding miRNA motifs from Exome sequencing
... the answer is no, exome seq only sequence known/targeted exon region ...
written 21 days ago by bharata1803360
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Comment: C: Bioinformatics conference with possible publication
... I am looking for international not only India area. ...
written 6 weeks ago by bharata1803360

Latest awards to bharata1803

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 4 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 4 months 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 Alternative sequence gene Ensembl ID
Popular Question 8 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 8 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 8 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 8 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 8 months ago, created a question with more than 1,000 views. For Comparison of microarray and RNA-seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For Salmon warning detected suspicious pair
Popular Question 8 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 8 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 10 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 10 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 11 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file

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