User: c.chakraborty

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c.chakraborty160
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Posts by c.chakraborty

<prev • 43 results • page 1 of 5 • next >
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Comment: C: How can I get true transcript_ids from StringTie?
... What annotation file (.GFF) did you have to map the transcripts? You need to use the GFF file used for mapping and the stringTie output which is also in .GFF. Use GFFcompare tool to get the ids for the transcripts. ...
written 8 months ago by c.chakraborty160
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Comment: C: total RNA-seq public data with rRNA
... You may search Array Express and GEO omnibus. Look at the protocol carefully and download the raw files according to your experimental question. Sorry for not being much of a help. ...
written 9 months ago by c.chakraborty160
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Comment: C: Analyzing LogRPKM Counts Data for finding DEGs(Differential Expressed Genes)
... Check if the dataset comes with raw read counts or not. I would suggest using EdgeR, Limma, DESeq2 for differential gene expression analysis. EdgeR / limma normalizes the count matrix based on the library size. It is not wise to use the normalized expression dataset you mentioned (RPKM - normalized ...
written 9 months ago by c.chakraborty160
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Comment: C: Processing gene expression data
... Go to the supplementary GSE1133_RAW.tar. Click on custom and it will lead you to all the .CEL files in this dataset. You can download whichever you need for your analysis. ...
written 9 months ago by c.chakraborty160
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Answer: A: Processing gene expression data
... Isn't there access to raw .CEL files for you to work on? Plus which paper, could you please share the link or doi.! I checked and there are .CEL files available for microarray analysis. If you want to analyse microarray data for gene expression analysis using, you should use the .CEL files. They are ...
written 9 months ago by c.chakraborty160
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Comment: C: .hic to .cool
... Yeah I did, I got a link to HiCompare and from that to HiC-pro, straw tool and also the HiC explorer. I am interested in running the data visualization tools from HiC explorer, so I am installing the requirements tools, but I was wondering if there was already a vignette in Bioconductor for data tra ...
written 10 months ago by c.chakraborty160
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.hic to .cool
... Hi everyone, Are there tools to convert format to transform `.hic` files to `.cool` or `.h5` files in R? Thanks in advance, Chai ...
R hic written 10 months ago by c.chakraborty160 • updated 10 months ago by zx87549.4k
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Answer: A: DESeqDataSetFromMatrix giving an error
... Check if your matrix is raw read counts. If it is normalized to the library, i.e counts would look like - 38.713, 410.006, then DESeqDataSetFromMatrix gives an error. DESeq2 is designed for raw read counts. ...
written 10 months ago by c.chakraborty160
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Answer: A: Meaningful DE using rpkm values in a RNA-Seq analysis
... Use raw read counts for genes and put them in DESeq2 or EdgeR for analysis. With RPKM, your expression is normalized to the length of the transcript. Thus if you have a very long transcript, the normalized value will be lower. As it is a practice in RPKM based analysis, to use a cutoff for expressio ...
written 11 months ago by c.chakraborty160
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Comment: C: How to get the position of a transcript on chromosome with ncbi refseq_ncrna id?
... Did you choose Refseq ncRNA ID from the dropbox menu? ...
written 13 months ago by c.chakraborty160

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