User: EagleEye

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EagleEye3.5k
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2 years, 8 months ago
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PhD student at University of Gothenburg. Most of my work involves designing or benchmarking pipelines for transcriptome and genomic sequencing data related to epigenetics and cancer.

Posts by EagleEye

<prev • 614 results • page 1 of 62 • next >
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Comment: C: How to get the number of exon within genes from GRCH37 reference
... Okay. Thanks a lot. ...
written 2 days ago by EagleEye3.5k
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Comment: C: How to get the number of exon within genes from GRCH37 reference
... Nice. I am just wondering, is there a way to get only non-coding regions directly from mysql ? ...
written 2 days ago by EagleEye3.5k
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Answer: A: How to get the number of exon within genes from GRCH37 reference
... This I made it in very rough way. But it works. The below command will give you number of exons per transcript of non-coding regions from Ensembl GTF file. http://ftp.ensemblorg.ebi.ac.uk/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz **Create Exon numbers file with transcript ID:** ...
written 2 days ago by EagleEye3.5k
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Comment: C: Differences between trimming tools: cutadapt, bbduk and sickle
... For choosing proper tools to remove adapters from your reads check [this article][1] (Table 1). [1]: https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-5-337 ...
written 4 days ago by EagleEye3.5k
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Answer: A: Retrieving data from Kegg
... [GeneSCF][1] is perfect for your task. Check [this post][2] for some example. Also check [this post][3] for general usage. [1]: https://www.biostars.org/p/108669/ [2]: https://www.biostars.org/p/231384/#231579 [3]: https://www.biostars.org/p/191532/#191540 ...
written 4 days ago by EagleEye3.5k
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Answer: A: organism choose of clusterProfiler
... Give it a try using [GeneSCF][1]. [1]: https://www.biostars.org/p/108669/ ...
written 5 days ago by EagleEye3.5k
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Answer: A: how to download sequences of gene product associated with certain GO term
... Try [GeneSCF][1] perl based (works on LINUX and windows 10 bash1607). GeneSCF can be used for - gene enrichment analysdis with your gene list - [Download complete terms and genes as plain text format][2] (TAB separated table) [1]: https://www.biostars.org/p/108669/ [2]: https://www.bio ...
written 7 days ago by EagleEye3.5k
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Answer: A: network analysis of differentially expressed genes
... I assume that you are asking about pathway enrichment analysis. Use your gene list (per condition) in [GeneSCF][1] using KEGG as a reference database. It will give you results with enriched KEGG terms in each condition. For presenation of the results please [check this post][2]. [1]: https:// ...
written 11 days ago by EagleEye3.5k
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Comment: C: How to create your own association file for gene ontology enrichment analysis ?
... Also have a look at [GeneSCF][1], if it works for you. **Note:** [Check this question regarding non-model organism and GeneSCF usage][2]. [1]: https://www.biostars.org/p/108669/ [2]: https://www.biostars.org/p/108669/#223241 ...
written 12 days ago by EagleEye3.5k
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Comment: C: Ingenuity Pathway Analysis Galaxy Dataset
... Hi, You can also use [GREAT][1] to associate your peaks to genes. GREAT will give you output with associated gene symbols to individual peaks. Those gene symbols can be used in GeneSCF to get enriched terms or biological process. **Note:** GeneSCF only works on Linux system, it has been successful ...
written 12 days ago by EagleEye3.5k

Latest awards to EagleEye

Teacher 15 hours ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Scholar 2 days ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 12 days ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
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Scholar 9 weeks ago, created an answer that has been accepted. For A: How to get all disease-causing genes from OMIM?
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