User: Y Tb

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Y Tb200
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USA
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2 years, 4 months ago
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6 years, 5 months ago
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Posts by Y Tb

<prev • 39 results • page 1 of 4 • next >
5
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Is there any differences between Human Genome downloaded from UCSC website and the on from Ensembl
... I am trying to use tophat to map RNA-seq data with human genome, I found that the human genome and different versions from annotation files are available under the following tab Index and annotation downloads at tophat website (http://ccb.jhu.edu/software/tophat/igenomes.shtml ). as shown in the ta ...
genome ensembl next-gen rna-seq ucsc written 5.6 years ago by Y Tb200 • updated 5.6 years ago by Emily_Ensembl21k
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Comment: C: What causes this message in IGV?
... Dear Daniel,  Thanks for your respond. Is there any way to use the same reference genome and same release or gtf file that I used in Tophat directly on IGV instead of using the defaults one on it. ...
written 5.8 years ago by Y Tb200
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What causes this message in IGV?
... I am trying to visulize rna-seq mapped data for mouse from Tophat results (accepted_hits.bam file). I used mm9 as a reference  genome in IGV. When I  looked for specific nmaes on this data, I can visulize some of them but the others not shown and IGV gave me the following message Cannot find feature ...
next-gen rna-seq sequencing written 5.8 years ago by Y Tb200
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What are the human and mouse reference genome (hg19, mm9) based on IGV?
... What are the human and mouse reference genome (hg19, mm9) based on IGV, I mean are those reference genomes based on Ensembl assembly or UCSC assembly. ...
genome next-gen rna-seq sequencing written 5.8 years ago by Y Tb200 • updated 5.8 years ago by Neilfws48k
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Comment: C: Error in IGV "Cannot find feature or locus: RP11-571E6.3"
... Dear Antonio, I used hg19 as a reference in Tophat, in addition, I used the gene model (annotation file .GTF file ) from ensemble . That is why I am looking for those genes names in my mapped data. ...
written 5.8 years ago by Y Tb200
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Error in IGV "Cannot find feature or locus: RP11-571E6.3"
... I am trying to visulize mapped data that I got from Tophat for RNAseq data using IGV, and I am looking to specific genes names on this data. I can visulize some of these genes but the other no and I got this error message in IGV "Cannot find feature or locus: RP11-571E6.3" BTW: I am using hg19 as ...
next-gen rna-seq sequencing written 5.8 years ago by Y Tb200 • updated 5.8 years ago by Antonio R. Franco4.5k
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How to create a genome from hg19.fa file and GTF file from ensembl to be use to visualize mapped data from tophat in IGV?
... I want to visualize mapped data that I got from Tophat (.bam file) and I want to use the genome that I provided in Tophat command line, but I noticed that there is an option in IGV allows user to create genome form a specific reference genome. The problem I faced that when I used the default genome ...
next-gen rna-seq written 5.8 years ago by Y Tb200
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Comment: C: Strand-specific vs.Non strand-specific in RNAseq
... Dear Albert, Could you please let me know what is the best way to detect antisense and count the reads (which sense and which antisense). My RNA-seq data are for  human/mouse.  ...
written 6.0 years ago by Y Tb200
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Comment: C: Strand-specific vs.Non strand-specific in RNAseq
... Dear Sam, Could you please send me the information about the procedure of the protocol because I am not biologist major and  I want to know more about it. Also, about the type of strand specific library. BTW, the discussion link doesn't work ...
written 6.0 years ago by Y Tb200
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5 follow
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Strand-specific vs. non-strand-specific RNAseq
... I want more details about Strand-specific vs. Non strand-specific protocols in RNAseq. I know that the benefit of strand-specific is to know whether the read originated from the +ve  or - ve strand, also it helps identify antisense RNA, and I know it costs more than non-strand-specific. So could you ...
next-gen strand-specific rna-seq written 6.0 years ago by Y Tb200 • updated 6.0 years ago by Malachi Griffith18k

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Student 2.7 years ago, asked a question with at least 3 up-votes. For What is the difference between GTF AND GFF format
Popular Question 2.8 years ago, created a question with more than 1,000 views. For What are the human and mouse reference genome (hg19, mm9) based on IGV?
Appreciated 3.4 years ago, created a post with more than 5 votes. For What is the difference between GTF AND GFF format
Great Question 3.8 years ago, created a question with more than 5,000 views. For What is the difference between GTF AND GFF format
Popular Question 3.8 years ago, created a question with more than 1,000 views. For What causes this message in IGV?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For What are the human and mouse reference genome (hg19, mm9) based on IGV?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For What is the difference between GTF AND GFF format
Great Question 4.8 years ago, created a question with more than 5,000 views. For What is the difference between GTF AND GFF format
Epic Question 4.8 years ago, created a question with more than 10,000 views. For What is the difference between GTF AND GFF format
Epic Question 4.8 years ago, created a question with more than 10,000 views. For Strand-specific vs. non-strand-specific RNAseq
Popular Question 4.8 years ago, created a question with more than 1,000 views. For What is the difference between refrence genome and annotation ?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For What is the difference between GTF AND GFF format
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Details About Fastqc Programs Results (Modules).
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Great Question 5.6 years ago, created a question with more than 5,000 views. For What is the difference between GTF AND GFF format
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Details About Fastqc Programs Results (Modules).
Popular Question 5.6 years ago, created a question with more than 1,000 views. For What is the difference between GTF AND GFF format
Popular Question 5.6 years ago, created a question with more than 1,000 views. For How To Get Full Information About Rna-Seq File?
Popular Question 5.6 years ago, created a question with more than 1,000 views. For What is the difference between refrence genome and annotation ?
Student 5.6 years ago, asked a question with at least 3 up-votes. For What is the difference between GTF AND GFF format
Popular Question 5.8 years ago, created a question with more than 1,000 views. For What is the difference between GTF AND GFF format
Popular Question 5.8 years ago, created a question with more than 1,000 views. For TopHat paramertes " -G/--GTF

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