User: ra2967

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ra296710
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Posts by ra2967

<prev • 11 results • page 1 of 2 • next >
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Comment: A: Limma can make differential expression with just one case in one group?
... Hello, Thanks, but the point discussed there or in the other discussion I have found it is not related to my question. I was asking the statistics that allow limma to do the analysis of 1 vs others, no the convenience of using replicates. We are obvoulsy working on them, but to the date we only hav ...
written 16 days ago by ra296710
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Limma can make differential expression with just one case in one group?
... Hello all, I have the normalized counts from RNA-Seq analysis in 6 populations. We are waiting for the triplicates, but I have discover that limma can do the differential expression analysis of the genes in one population vs the others (and the results seems to work pretty well!). Is it statisticall ...
differential expression limma rna-seq written 19 days ago by ra296710 • updated 16 days ago by Gordon Smyth470
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Answer: A: Stringtie elimination of important transcripts
... Thank you all, However, if this was the case, I would not have any "zero coverage"/ zero FPKM in my final gtf. In all my gtf (one per sample) I have transcripts that have zero FPKM, and they are not removed. Regarding the merge algorithm, we performed it and we are not recovering this gene in the ...
written 4 weeks ago by ra296710
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Comment: A: Stringtie elimination of important transcripts
... I answer it on the bottom ...
written 4 weeks ago by ra296710
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Stringtie elimination of important transcripts
... Dear all, I have nine RNA-Seq files that I aligned using the hisat2 aligner and this default command: hisat2 -x grch37_snp_tran/genome_snp_tran -1 reads_R.fastq.gz -2 reads_F.fastq.gz -S sample.sam The -x file was the one they recommened in the hisat2 website. Files looked fine and I proceed to ...
assembly stringtie alignment rna-seq hisat2 written 5 weeks ago by ra296710
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Comment: C: Find the distance between motif in a group of fast sequences
... In each one of my fasta sequences, they are distributed in different position. I would like to know the distance in each sequences that separate the motif A and the motif B, what may be not the same. As I told, it may be solved by "text analysis", but I do not know how. ...
written 3 months ago by ra296710
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Find the distance between motif in a group of fast sequences
... Hi all, I have a list of one hundred sequences. I know using MEME that my sequences all have two conserved motifs for two transcriptions factors. My question is: may I calculate the distance of one motif to the other for each one of the sequences? I think that these proteins are interacting and th ...
motif analysis chip-seq written 3 months ago by ra296710
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Comment: A: Normalization Method In Comparing Differential Gene Expression
... Hello! Thanks for the comments. Must you eliminate those probes that are always zero in all your samples before doing the normalization or it is not necessary? ...
written 6 months ago by ra296710
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GSEA top genes vs all platform
... Hello, I have done an analysis in LIMMA to obtain the differential expressed genes. However, now I have 2 questions when I perform GSEA: - Must I order my samples by fold change (first negative and after positive forld change, por example) in a preranked analysis? Is it better to order by p.val? C ...
functional analysis rna-seq gsea written 6 months ago by ra296710 • updated 6 months ago by Charles Warden6.1k
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Comment: A: Create an assembly with a ribosomic chromosome
... Thanks! I am interested in seeing if my samples bind (ChIP-Seq) and the status of the chromatin (ATAC-Seq) in this chrosomome, but I see how they do here in the paper and finally it was not very difficult. ...
written 6 months ago by ra296710

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