User: caggtaagtat

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caggtaagtat930
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Posts by caggtaagtat

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Comment: C: Whats best practice for Gene set enrichment analysis?
... Thank you, I will give this a try. ...
written 1 day ago by caggtaagtat930
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Whats best practice for Gene set enrichment analysis?
... Hi, I would like to know how you do GSEA for human or mouse samples. Which tool do you use and how to you visualize it? ...
gsea written 1 day ago by caggtaagtat930 • updated 1 day ago by EagleEye6.6k
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Comment: C: Is it possible to obtain all the RefSeq transcripts of Ensembl genes for GRCh37
... I know, that there was a mixup in your question. I just wanted to answer it anyway, in case someone needs it. From the link, you get to the old biomart with transcript coordinates in reference to the GRCh37 genome. Like in the normal biomart, you can select as attributes, the RefSeq ID per ENSEMBL ...
written 5 weeks ago by caggtaagtat930
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Answer: A: Is it possible to obtain all the RefSeq transcripts of Ensembl genes for GRCh37
... Hi, [here][1] is the link for biomart of the GRCh37 genome, in case someone did not find the link. You can get to every version through ensembl archives. [1]: https://grch37.ensembl.org/biomart/martview/ebf63d04a3e464273114aa772f2c7b98 ...
written 5 weeks ago by caggtaagtat930
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Answer: A: STAR alignment EXITING because of FATAL ERROR: could not create output file
... Hi, I think the argument `--outFileNamePrefix` wants to have a directory as an input, where the results of STAR will be saved. If you just do this STAR run, I would first create the output directory mkdir 65312-RNA-FFPE and then execute STAR with this parameter: --outFileNamePrefix /home ...
written 10 weeks ago by caggtaagtat930
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Answer: A: Identification of Human Genes ?
... If your pc is not restricted by a firewall, you can use the R package biomart to access the gene names listed in ensembl.org for humans. [Here][1] is the link for the manual [1]: https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html ...
written 3 months ago by caggtaagtat930
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Answer: A: Cis-regulatory motif discovery from RNA-Seq
... I don't think this is possible on a global scale. In case I understood your question right, that you would like to finde motifs which not completly turn off transcription but reduce transcription of certain transcripts, than I would say, this is not possible at the moment. When you sequence RNA, ...
written 3 months ago by caggtaagtat930
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Comment: C: snakemake: pipeline failed with MissingOutputException
... Ok, than I think an alternative solution could be to submit the jobs similar to this, depending on the "job scheduler" on your cluster ...
written 3 months ago by caggtaagtat930
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Comment: C: snakemake: pipeline failed with MissingOutputException
... I see. You can simualte a "clsuter" on your mashien, thats why I got confused about. You are right, the OP want to execute it on a regular cluster, so my answer is still relevant. Coming back to your question above: When you had 100 samples this snakemake script would try to submit 100 job to the c ...
written 3 months ago by caggtaagtat930
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Comment: C: snakemake: pipeline failed when submit to cluster
... Please excuse me, I was under the impression, that you wanted to submit the jobs to an High-Performing-Cluster. I just re-read your question and saw that you want to execute it on your local mashine. ...
written 3 months ago by caggtaagtat930

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Popular Question 24 days ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 3 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Scholar 3 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 5 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: How to create custom gtf annotation file?
Popular Question 7 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis
Popular Question 9 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Appreciated 10 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Scholar 10 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 10 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Scholar 11 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 12 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 12 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Popular Question 15 months ago, created a question with more than 1,000 views. For STAR do i need --twopassMode ?
Scholar 16 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
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Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?

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