User: ra2967
ra2967 • 20
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Posts by ra2967
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... Hello all,
I am a postdoc in Columbia University trying to install HiC pro. I dowloaded and installed all the dependencies, but when I try to run the install command 'make configure' in the folder where I unzipped the HiC pro pipeline, I obtained this message:
export /Users/Robert/anaconda3/bin/bo ...
written 6 weeks ago by
ra2967 • 20
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... 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 6 months ago by
ra2967 • 20
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... 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 ...
written 6 months ago by
ra2967 • 20
• updated
6 months ago by
Gordon Smyth • 950
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... 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 7 months ago by
ra2967 • 20
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... I answer it on the bottom ...
written 7 months ago by
ra2967 • 20
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... 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 ...
written 7 months ago by
ra2967 • 20
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... 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 9 months ago by
ra2967 • 20
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... 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 ...
written 9 months ago by
ra2967 • 20
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... 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 12 months ago by
ra2967 • 20
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... 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 ...
written 12 months ago by
ra2967 • 20
• updated
12 months ago by
Charles Warden ♦ 7.2k
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