User: Jon
Jon • 110
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Posts by Jon
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... 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 ...
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... That's what happened. There are more reads than I expected. ...
written 6 weeks ago by
Jon • 110
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5 follow
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... 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 ...
written 7 weeks ago by
Jon • 110
• updated
6 weeks ago by
caggtaagtat • 750
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... 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
Jon • 110
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... UCSC ................... ...
written 7 weeks ago by
Jon • 110
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... 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
Jon • 110
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... 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 ...
written 7 weeks ago by
Jon • 110
1
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...
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
Jon • 110
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239
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... 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
Jon • 110
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... 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
Jon • 110
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For BWA MEM vs BOWTIE2 , which is best?
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For How to overcome "duplicate row.names" error while importing tpm/count/fpkm matrix/table in R ?
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For how to sum up the columns to remove the duplicated row names in RSEM output?
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For converting paired end reads to single end, is this a good idea?
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For BWA MEM vs BOWTIE2 , which is best?
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For ERR: Perplexity is too large in Reducedimension step in Monocle
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