User: kanwarjag

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kanwarjag840
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United States
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Joined:
5 years, 2 months ago
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Posts by kanwarjag

<prev • 306 results • page 1 of 31 • next >
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identification of cell lineage tools
... Is there a tool that can help me to identify cell lineage from differential expression of genes? Thanks ...
rna-seq written 28 days ago by kanwarjag840 • updated 27 days ago by igor5.2k
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Comment: A: pathway for single cell RNA-seq
... I have already analyzed the data and has top differentially expressed genes specific for each cluster. Instead of using known markers I want to use enrichment/ pathway analysis that what type of cells are in each cluster. Apology If my original question was not explained clearly. ...
written 28 days ago by kanwarjag840
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pathway for single cell RNA-seq
... I have a single cell RNA-seq data form 10X genomics. I want to perform pathway analysis of top 50 genes of each cluster on the the basis of DE. These clusters represent cells with similar expression of genes. So in pathway analysis of these top 50 genes I want to identify what possible type of cell ...
pathway written 28 days ago by kanwarjag840 • updated 27 days ago by igor5.2k
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Comment: C: Question about Colon and small intestine size
... This appears to be a high school assignment. Try to google all this. ...
written 9 weeks ago by kanwarjag840
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Question about generalized linear model fitting
... I am analyzing a scRNAseq data trying to follow a protocol suggested in this paper- https://www.nature.com/articles/nature24489 mentioned under Computational analysis The statement reads- " Selection of variable genes was performed by fitting a generalized linear model to the relationship between t ...
rna-seq written 9 weeks ago by kanwarjag840 • updated 9 weeks ago by Kevin Blighe12k
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ScRNAseq and mitochondrial genes
... In single cell RNA seq mitochondrial (percentage of total expressed genes) is taken as a control. It is considered that less percentage of mitochondrial genes is indicative of good quality data. I could not find any rational when I google it or reading recent ScRNA-seq papers. Any pointer will be v ...
rna-seq written 9 weeks ago by kanwarjag840
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Comment: C: iontorrent RNAseq alignment
... TMAP is quite frequently used (https://github.com/iontorrent/TMAP) However I have used successfully TopHat (now HISAT). ...
written 10 weeks ago by kanwarjag840
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Question about a plot of RNAseq
... I was wondering is there any tool or method that can generate Fig 5A of https://www.nature.com/articles/ncomms14049?WT.feed_name=subjects_genetics. I know it is generated in moncole/ cell ranger/ surat, however if I have matrix than i may be able to draw it with any other tool and may have control ...
rna-seq written 10 weeks ago by kanwarjag840
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Question about mapping motif binding sites to genome location
... I have a naïve but complex question. I used RSAT to get 5 genes -2000 bp upstream sequence of TSS. I used this FASTA file and binding motif (identified from my experiment) in FIMO to see where is the binding site of the identified motif. I know that protein of interest bound very close to TSS. I g ...
genome written 4 months ago by kanwarjag840 • updated 12 weeks ago by Biostar ♦♦ 20
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Ncrna in cufflink analyzed RNA-seq
... I ran RNA- seq analysis through cufflink to cuff diff . I looked in various files but could not see lincRNA/ ncRNA any suggestion in which file I should be looking them Thanks ...
rna-seq written 4 months ago by kanwarjag840 • updated 4 months ago by Kevin Blighe12k

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