User: Jon

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Jon110
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Posts by Jon

<prev • 115 results • page 1 of 12 • next >
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Is it necessary to do FastQC before using RSEM?
... Hi When I see High profile journals, some of them ran FastQC, TrimGalore , Trinity for pre-processing fastq files of RNA seq reads, some of them didn't. Is it really necessary to do preprocessing (or) we can use raw fastq files in RSEM? Thank you in advance ...
R alignment rna-seq written 2 days ago by Jon110 • updated 2 days ago by genomax71k
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Comment: C: How to create custom gtf annotation file?
... That's what happened. There are more reads than I expected. ...
written 6 weeks ago by Jon110
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How to create custom gtf annotation file?
... Hi I am using RSEM (with bowtie2) for alignment then gene count. Using Refseq Annotation (gff3), and genomic.fna reference Fasta file from NCBI. RSEM can convert gff3 to gtf file. How can I subset the GTF file (or gff3 file) by gene a name. I want to extract the annotation (gtf) for particular gen ...
genome R rna-seq written 7 weeks ago by Jon110 • updated 6 weeks ago by caggtaagtat750
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Answer: A: How to Align only few transcript and get count?
... What I found: We should use Refseq reference genome and Gff3 annotation file for alignment. SO we will get Refseq Transcript ID details in here. ...
written 7 weeks ago by Jon110
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Comment: C: How to Align only few transcript and get count?
... UCSC ................... ...
written 7 weeks ago by Jon110
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Comment: C: How to Align only few transcript and get count?
... It's not even listed in the isoform list (there's only one isoform is in the result table). Thank you ...
written 7 weeks ago by Jon110
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How to Align only few transcript and get count?
... Hi, I have Two questions. I did RSEM for my (single-end) RNA seq reads. For a gene, I got isoform count for only one transcript variant. But I see three transcript variants in NCBI Nucleotide search. May I Know Why? (I used mm9 reference transcriptome for alignment using bowtie2 within RSEM) So No ...
R next-gen rna-seq written 7 weeks ago by Jon110
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Comment: C: Differential network analysis for two treatments
... What I did is: Find DE genes between control vs positive treatment, control vs negative treatment. Then I subset the common genes in both, the I plotted heat map, I got what I wanted. It worked for now. Will try to do it in proper way. Thanks for all the answers. ...
written 7 weeks ago by Jon110
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Comment: C: Differential network analysis for two treatments
... Hi Kevin, I have a count matrix from RSEM, triplicated samples for all three conditions. Sorry about lacking information. Can you check my updated question. Thanks for your answer. ...
written 8 weeks ago by Jon110
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Comment: C: Differential network analysis for two treatments
... thank you, > `assays(vsd)` gave me the variable genes between samples, I have three samples per condition. I need variable genes per group, not samples. Any idea? ...
written 8 weeks ago by Jon110

Latest awards to Jon

Popular Question 7 weeks ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 4 months ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 4 months ago, created a question with more than 1,000 views. For bwa mem has more MAPQ values as 0 and 60
Popular Question 4 months ago, created a question with more than 1,000 views. For MAPQ values are 60 in bwa mem
Centurion 4 months ago, created 100 posts.
Popular Question 17 months ago, created a question with more than 1,000 views. For How to get --transcript-to-gene-map in RSEM?
Popular Question 17 months ago, created a question with more than 1,000 views. For bwa mem has more MAPQ values as 0 and 60
Popular Question 17 months ago, created a question with more than 1,000 views. For how to sum up the columns to remove the duplicated row names in RSEM output?
Popular Question 17 months ago, created a question with more than 1,000 views. For converting paired end reads to single end, is this a good idea?
Popular Question 17 months ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 17 months ago, created a question with more than 1,000 views. For ERR: Perplexity is too large in Reducedimension step in Monocle
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