User: Ron

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Ron600
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Posts by Ron

<prev • 288 results • page 1 of 29 • next >
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Answer: A: rRNA detection (for contamination) in RNA-seq
... I used RseQC for rRNA detection. They have a bed file too. http://rseqc.sourceforge.net/ ...
written 9 days ago by Ron600
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Comment: C: HtSeq count error
... No,I had to revert back to the older version.The newer version still giving me the issue. I think BAM file needs to be modified,in order to get it working with the newer version. ...
written 28 days ago by Ron600
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Comment: A: HtSeq count error
... The bam file is working fine with older HTSEQ version 0.6.1, which I was using previously. So I reverted back. ...
written 29 days ago by Ron600
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Comment: C: gene set enrichment analysis for continuous phenotype
... Can you explain more on the continuous outcome? ...
written 29 days ago by Ron600
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Answer: A: Analysis ready RNA Seq repository
... GDC has cancer data processed. There are 11k samples. https://portal.gdc.cancer.gov/ ...
written 29 days ago by Ron600
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Answer: A: next step after differential expression analysis
... You can do pathway enrichment using GSEA http://software.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html GSEA pre-ranked requires complete list of genes with fold changes. you can chose signatures of interest and see if they are enriched. ...
written 29 days ago by Ron600
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HtSeq count error
... Hi all, I updated to new htseq count and am getting these errors. I was using previous version 0.6.1 and it was working well. Error occured when reading beginning of SAM/BAM file. 'pysam.csamtools.AlignedRead' object has no attribute 'reference_start' [Exception type: AttributeError, raised in ...
htseq-count rna-seq written 29 days ago by Ron600
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Answer: A: Post alignment QC of RNA-seq data
... Post alignment ,you can use rseqc, http://rseqc.sourceforge.net/ It has very good modules,to work with BAM. Also ,if you use STAR for alignment,please look out the log.final.out file for QC metrics. ...
written 29 days ago by Ron600
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Comment: C: Xenopus genome files for RNAseq
... Try checking the links I pasted above.These are xenbase links only. ...
written 29 days ago by Ron600
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Answer: A: Xenopus genome files for RNAseq
... I would use this file for the X. laevis 9.1 genome https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.xenbase.org_pub_Genomics_JGI_Xenla9.1_Xla.v91.repeatMasked.fa.gz&d=DwMFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=pt2eBGtCyE_Qi6slO5RVtfGA3zOwk4_M88OXcU9-nJI&m=kUg0RuM_AE ...
written 4 weeks ago by Ron600

Latest awards to Ron

Popular Question 13 days ago, created a question with more than 1,000 views. For Working with human database in Kraken
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Database of Ligand and receptor genes
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Database of Ligand and receptor genes
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Student 4 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 4 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 6 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Great Question 7 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 7 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 7 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 8 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
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Popular Question 10 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 12 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 13 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
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Popular Question 15 months ago, created a question with more than 1,000 views. For Clustering of genes using FPKM
Popular Question 16 months ago, created a question with more than 1,000 views. For htseq-count for RNA Seq
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Popular Question 19 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
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Student 19 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 21 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ

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