User: snp87

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snp8740
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Posts by snp87

<prev • 30 results • page 1 of 3 • next >
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Comparing transcriptomes of 3 samples
... Hello! I am comparing the transcriptomes of 3 types of cells, I'll call them A1, A2 and B for convenience. What would be the best way to see the relationship between the transcriptomes (i.e which 2 populations have the most variance and which 2 populations have the least variance and so on)? I did t ...
venn diagram rna-seq written 12 months ago by snp8740
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Comment: C: Comparing FPKM values in different genes
... Thanks so much for the suggestion - I will try that ...
written 12 months ago by snp8740
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Comment: A: Comparing FPKM values in different genes
... Thanks so much for your reply, Kevin. You make some valid points. Just a few clarifications, though. My purposes for RNA-seq was to perform a differential expression analysis between 2 group of closely related cells. While that was the main aim, now that I have the datset, I want to see what method ...
written 12 months ago by snp8740
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Comparing FPKM values in different genes
... Hi all, I am new to RNA-seq analysis and I wanted to ask about comparing expression in different genes. I apologise in advance that this question is quite basic. I used Cuffdiff to perform a differential expression analysis and validated several candidate genes identified using in situ hybridisatio ...
validation of genes rna-seq written 12 months ago by snp8740 • updated 13 days ago by Morris_Chair120
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Comment: C: Fasta file and GTF file for STAR alignment
... Thanks for your reply. I'm not sure if I understand what you mean. I'm hoping to do a differential expression analysis after the alignments. In the fasta files there were different options, cdna, cds, dna, dna index, ncrna and pep (ftp://ftp.ensembl.org/pub/release-92/fasta/mus_musculus/). I went wi ...
written 16 months ago by snp8740
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Fasta file and GTF file for STAR alignment
... Hello, this is a very basic question but I was wondering if someone could help me understand if I've used the correct GTF file and Fasta file for the mouse genome indexing (I'm using STAR). I got the relevant Fasta file and GTF file from ensembl: Mus_musculus.GRCm38.92.gtf.gz from ftp://ftp.ensembl. ...
ensembl star written 16 months ago by snp8740 • updated 15 months ago by swbarnes26.5k
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Identifying TFs from a list of genes
... Hello! Is there a way I can feed a list of genes generated from a RNAseq experiment and find out which ones are transcription factors? This is in mouse. Any help is much appreciated. ...
gene rna-seq written 22 months ago by snp8740 • updated 22 months ago by svlachavas580
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stoping a TopHat alignment
... Hi, I'm trying to stop a TopHat alignment (my computer is low in memory and the run is failing to report the final output (it's been stuck at that stage for about 20 hours now and usually the whole alignment would only take around 6 hours). Is there a way I could stop that particular alignment witho ...
rna-seq written 2.3 years ago by snp8740
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Getting a list of genes expressed
... Hello! I am trying to look at genes that are expressed in a population of cells without comparing to another cell's transcriptomic data (obtained through RNAseq). Does anyone have any suggestions for which tool might be best to get a list of genes that are expressed sorted according to expression le ...
rna-seq transcriptome written 3.2 years ago by snp8740 • updated 3.2 years ago by Devon Ryan92k
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Comment: C: Running cufflinks - gtf file not recognised
... Thanks for the suggestion. I'm getting a segmentation fault 11 error when using that command. > [14:59:11] Loading reference annotation. > No fasta index found for Mus_musculus.GRCm38.dna.toplevel.fa. Rebuilding, please wait.. > Fasta index rebuilt. > [15:04:36] Inspecting reads and ...
written 3.2 years ago by snp8740

Latest awards to snp87

Epic Question 12 months ago, created a question with more than 10,000 views. For generating genome indexes with STAR
Popular Question 19 months ago, created a question with more than 1,000 views. For Running cufflinks - gtf file not recognised
Popular Question 19 months ago, created a question with more than 1,000 views. For Cufflinks segmentation fault
Great Question 2.3 years ago, created a question with more than 5,000 views. For generating genome indexes with STAR
Popular Question 2.3 years ago, created a question with more than 1,000 views. For aligning with STAR
Popular Question 3.2 years ago, created a question with more than 1,000 views. For aligning with STAR
Popular Question 3.2 years ago, created a question with more than 1,000 views. For generating genome indexes with STAR
Student 3.2 years ago, asked a question with at least 3 up-votes. For generating genome indexes with STAR

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