Moderator: EagleEye

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EagleEye5.7k
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Sweden
Website:
https://decodebiology....
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gridhrahakshi
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Last seen:
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4 years, 2 months ago
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 886 results • page 1 of 89 • next >
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Comment: C: HUGO and Ensembl ids
... Please provide some examples. ...
written 18 hours ago by EagleEye5.7k
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Comment: C: Problem with extracting read counts from RNA seq file
... Hi, in SAM/BAM format **third-columns** are chromosome names. In this case third column has to match with chromosome names in GTF/GFF3. ...
written 1 day ago by EagleEye5.7k
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Comment: C: Problem with extracting read counts from RNA seq file
... Sorry other than that I could not see any problem. It is is hard to figure out when you do not get any errors. can you post few lines from your GTF file ? ...
written 2 days ago by EagleEye5.7k
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Comment: C: Problem with extracting read counts from RNA seq file
... Looks like your BAM and GTF files individually does not have any issue. Sometimes this happens when the chromosome names are not matching between BAM and GTF files (Example, "chr12" or "12"). ...
written 2 days ago by EagleEye5.7k
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Comment: C: Gene ontology and KEGG pathway analysis of rice RNA-seq data
... Hi afli, Thanks for you comment. Since geneSCF has to maintain some standard nomenclature, geneid always refers to Entrez geneid and anything other than entrezid (such as gene names containing characters rather than just numbers) must be considered as gene symbol. **Example:** Oryza sativa japon ...
written 3 days ago by EagleEye5.7k
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Answer: A: Plot to show expression of a gene between two groups
... Simple way to plot is, boxplot(eg$GeneA~eg$Type,ylab="GeneA (logCPM)", outcol="white") stripchart(eg$GeneA~eg$Type, vertical = TRUE, data = eg[,c(2:3)], method = "jitter", add = TRUE, pch = 20, col = 'blue') ...
written 15 days ago by EagleEye5.7k
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Answer: A: Sorting RNA-seq data
... If you are using Microsoft Excel, =IF(AND(A1D1),"YES","NO") ...
written 16 days ago by EagleEye5.7k • updated 16 days ago by zx87545.4k
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Comment: C: what is the easiest/fastest way to convert from BAM to GTF
... What do you mean by BAM to GTF ? There is no direct connection between BAM and GTF. You usually quantify genes from GTF (gene annotation) by using BAM file (alignment) as input. What is your goal ? Are you planning to do transcript assembly (in that case you can go for Cufflinks which generated GTF ...
written 16 days ago by EagleEye5.7k
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Answer: A: Run a GO analysis for an non-model organism with annotation file
... Check out this post https://www.biostars.org/p/108669/#223241 ...
written 25 days ago by EagleEye5.7k
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Answer: A: Extract a chromosome from a WIG file
... Try IGV '[toTDF][1]' to convert your 'WIG' files into binary tiled data (TDF). This loads into IGV lot faster than 'WIG' files. [1]: https://software.broadinstitute.org/software/igv/igvtools_commandline ...
written 26 days ago by EagleEye5.7k

Latest awards to EagleEye

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Scholar 4 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 4 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?

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