User: super

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super50
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Posts by super

<prev • 43 results • page 1 of 5 • next >
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News: 4th Annual Viral Genomics & Bioinformatics Training Course (20-24 August 2018)
... The MRC-University of Glasgow Centre for Virus Research (CVR) has been running a successful training course on Viral Bioinformatics and Genomics annually since 2015 and applications are now open for the 2018 course. We will be giving a 5-day course, which will consist of a series of lectures and pr ...
next-gen genomics news course bioinformatics virus written 10 months ago by super50
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Comment: C: metaViC: Virus metagenomics pipeline for unknown host or in absence of a host ge
... I think it is a brilliant pipeline ! ...
written 2.2 years ago by super50
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Answer: A: Error For End Coordinate When Running Cuffdiff
... Hi I have same problem with you! It seems that lots of people have this error. I use the Ensembl genome(***dna.toplevel.fa) and GTF file. If I ran cufflinks (even without -b genome.fa) but then run Cuffmerge with -s genome.fa, I got the error! If I omitted -b genome.fa in both Cufflinks and Cuff ...
written 2.5 years ago by super50
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htseq-count error RNAME == '*' although flag bit &0x0004 cleared"
... Hi all I do rna-seq , after tophat mapping, I got 6 aligned.bam file . And I played them by Cuffdiff, it works. However, if I try Htseq-count on 6 aligned.bam file (I have sorted and transfer it to SAM), one of them have error and hence I cannot get the counts table. The error is Error occured ...
next-gen rna-seq written 2.6 years ago by super50
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Comment: C: Current state-of-the-art for RNA-Seq gene / transcript expression quantification
... If not big difference between "Tophat+Cufflinks+Cuffmerge+Cuffdiff" and "Tophat+Cuffdiff" , I 'd like to ignore Cufflinks cause it is more time -consuming. :) ...
written 2.6 years ago by super50
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Comment: C: Current state-of-the-art for RNA-Seq gene / transcript expression quantification
... Hi Devon I remember I read lots of post talking about we could run Tophat+Cuffdiff (without Cufflinks+Cuffmerge) if we don't want find novel gene (just use reference gonome's GTF file) in analysis. I don't want look at novel gene from merged.gtf, but I want to know if there is big difference betw ...
written 2.6 years ago by super50
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Answer: A: gffread cannot get the gene symbol name for each transcript
... anybody knows the answer? Thank you ...
written 2.6 years ago by super50
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gffread cannot get the gene symbol name for each transcript
... Hi All When I run gffread to get transcripts from Tophat output cufflinks -p 8 -u -g reference_genome_genes.gtf -o outdir accepted_hits.bam cd outdir gffread -w transcripts.fa -g reference_genome.fa transcripts.gtf I got the transcripts.fa. >CUFF.5657.1 gene=CUFF.5657 &g ...
genome cufflinks rna-seq transcriptome written 2.6 years ago by super50
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Answer: A: Should adapters for RNASeq be removed before alignment?
... The reads need to be trimmed. -m is the distance for setting. you need set -r/--mate-inner-dist parameter when you want to do Tophat. ...
written 2.6 years ago by super50
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Answer: A: Cummerbund Returns 0 Sample
... I have similar questions but no one knew the answers. **CuffSet instance with: 2 samples 25264 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS** but I have 6 samples (3 samples in 1 group), I don't know why it h ...
written 2.7 years ago by super50

Latest awards to super

Popular Question 16 months ago, created a question with more than 1,000 views. For how to add a pseduo gene into a GTF file?
Popular Question 20 months ago, created a question with more than 1,000 views. For Gene ID conversion and Pathway analysis after mosquito blast
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to get the expression level of specific gene without annotation in RNA-Seq?

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