Moderator: EagleEye

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EagleEye6.0k
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https://decodebiology....
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

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Comment: C: Pathway analysis and Gene enrichment Analysis Queries
... Adding to the list, Command-line based: https://www.biostars.org/p/108669/ ...
written 6 days ago by EagleEye6.0k
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Answer: A: HUGO and Ensembl ids
... Hi, Only last one is from chromosome 22 assembly. The first 2 are from the exception contigs (haplotype variant contigs). So there is a reason to assign different 'ENSG' names for them. I would say always use 'ENSG' ids as reference/indexing purpose, when you are working with ensembl annotation. I ...
written 27 days ago by EagleEye6.0k
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Answer: A: Chip-seq data of bivalent regions in hESC
... You can find it yourself from [ENCODE deposited hg19 processed ChIP-seq data][1]. You can find BED files for both H3K4me3 and H3K27me3. [1]: https://www.encodeproject.org/search/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assembly=hg19& ...
written 27 days ago by EagleEye6.0k
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Answer: A: How can implement ensembl gene annotation pipeline for my data?
... You may convert your ensembl GTF into gene-based annotation table (tab-delimited). Then you can import this simple table in R or just use linux command-line tools to annotated your results. Check out this post https://www.biostars.org/p/140471/#140798 ...
written 29 days ago by EagleEye6.0k
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Answer: A: limitations of Edge R or DEseq
... Hi, answer to your question - check out these articles, [A comparison of methods for differential expression analysis of RNA-seq data][1] [Evaluation of methods for differential expression analysis on multi-group RNA-seq count data][2] [RNA-Seq differential expression analysis: An extended revie ...
written 4 weeks ago by EagleEye6.0k
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Comment: C: How can i extract FPKM from my GTF file which is created by stringtie?
... It is not always the case. There are also cases like this where it depends on the quantification approach, ![enter image description here][1] [Image publication ref][2] [1]: https://www.omicsonline.org/articles-images/next-generation-sequencing-applications-Illustration-gene-quantification-met ...
written 4 weeks ago by EagleEye6.0k
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Answer: A: How can i extract FPKM from my GTF file which is created by stringtie?
... Form StringTie output you can use 'sample1_**gene_abund.tab**' file to extract these information, **FPKM:** cat {sample1}_gene_abund.tab | cut -d$'\t' -f1,8 | sed "s/FPKM/sample1_FPKM/" | sed 's/Gene ID/gene_id/' > {sample1}_gene_abund.fpkm.txt **TPM:** cat {sample1}_gene_abund.tab ...
written 4 weeks ago by EagleEye6.0k
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Comment: C: hisat2 and RSEM pipeline
... Oops sorry that didn't work. I just checked output from this pipeline, I never succeeded in integrating HISAT2 + RSEM. Looks like [RSEM cannot handle gapped alignments][1]. [1]: https://github.com/alexdobin/STAR/issues/349 ...
written 4 weeks ago by EagleEye6.0k
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Answer: A: hisat2 and RSEM pipeline
... This is the way I could integrate HISAT2 with RSEM, **RSEM pre-preparation**: cat Homo_sapiens.GRCh38.90.chr.gtf | grep -v "^#" | grep -w "transcript" | cut -f9 | sed 's/;/\t/g' | cut -f1,3 | sed 's/gene_id \"//' | sed 's/transcript_id \"//' | sed 's/\"//g' | awk '!x[$0]++' > transcript_gen ...
written 4 weeks ago by EagleEye6.0k
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Comment: C: eQTL analysis considering P-values
... In simple terms as I understood, -------- **Differential expression analysis:** Finding difference in expression between two groups/tissues. **eQTL:** Association of SNPs/polymorphisms with expression in specific/different tissues OR finding the effect of SNPs/polymorphisms on expression in spec ...
written 5 weeks ago by EagleEye6.0k

Latest awards to EagleEye

Commentator 10 days ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Appreciated 21 days ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Scholar 4 weeks 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?
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 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Scholar 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
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 6 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 6 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 6 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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