User: ms5168

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ms51680
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Posts by ms5168

<prev • 10 results • page 1 of 1 • next >
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GC and Rik genes
... Hello, I ran an RNA-Seq analysis using Cufflinks. After finishing the analysis I got a long list of GC and Rik (followed by numbers) genes, along with regular annotated genes. Any idea what these genes are? Thanks ...
cufflinks rna-seq written 18 months ago by ms51680 • updated 18 months ago by Mo Heydarian790
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cuffdiff tabular file conversion
... Hello, I just finished running differential expression analysis using cuffdiff. The end result is in a tabular file format. I would like to do some further manipulation with the data. Is there a way to convert the tabular file to an excel file or something else other than fasta? Thank you, Moti ...
cuffdiff tabular excel format convert written 18 months ago by ms51680 • updated 16 months ago by Jennifer Hillman Jackson23k
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Answer: A: Cuffmerge fails to merge gtf files
... Hi, Just the assembled transcripts ...
written 18 months ago by ms51680
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Cuffmerge fails to merge gtf files
... Hello, I am trying to merged to assembled transcripts produced by cufflinks using cuffmerge. I am getting the following error message: merge_cuff_asms v1.0.0 cuffmerge -o cm_output -p 6 -g /galaxy-repl/main/files/016/369/dataset_16369716.dat --min-isoform-fraction 0.05 /galaxy-repl/main/jobdir/ ...
cufflinks written 18 months ago by ms51680
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Answer: A: Rna-Sea analysis and cufflinks
... Thank you very much, Jennifer. This is very helpful. I have another issue. I ran the following pipeline: Alignment -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund (failed) After running Cufflinks, I checked to see that there are FPKM values in the "transcript.gtf" files and that ...
written 18 months ago by ms51680
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Answer: A: Rna-Sea analysis and cufflinks
... Thank you for the prompt reply, Jennifer. I recently started to work in this lab. All the RNA preps were created and sent for sequencing prior to my arrival. Some directories have one fastq file while others have 2. Can I assume that the directories with 2 files are pair-end and the ones with 1 fil ...
written 18 months ago by ms51680
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Answer: A: Rna-Sea analysis and cufflinks
... It works greatly, thank you. One more question, how can I tell if my sequence data is single-end or paired-end? Thank you very much ...
written 18 months ago by ms51680
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Rna-Sea analysis and cufflinks
... Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gene expression: FASTQ Groomer -> TopHat -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund Do I miss anything in the pipeline or this is the correct workflow for gene expression analysis? ...
cufflinks cuffmerge rna-seq written 18 months ago by ms51680
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Comment: C: Keep getting "This is a new dataset and not all of its data are available yet"
... Thank you for your response, Jen. You were right, the job was successfully completed after a while. However, I have another issue. I tried to run MAP with BWA and got the following error message: An error occurred with this dataset: Fatal error: Exit code 1 () (33, "HTTP server doesn't seem to supp ...
written 19 months ago by ms51680
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Keep getting "This is a new dataset and not all of its data are available yet"
... Hi there, I am keep getting the message "This is a new dataset and not all of its data are available yet". nothing is in the queue. It happened both in FASTQ Groomer and TopHat. Is there anything wrong with the file? Thank you in advance, Moti ...
tophat rna-seq written 19 months ago by ms51680 • updated 5 months ago by megan_overton0

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