User: rkp21

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rkp2120
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2 years, 2 months ago
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r****@pitt.edu

Posts by rkp21

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Cuffdiff Fatal error: Matched on error
... Hi Jen, If I specify "report alignments specifically tailored for cufflinks" I am able to remove the XS tag error. However I still haven't been able to successfully run Cufflinks. I'm actually running into a different error now which I describe here: https://biostar.usegalaxy.org/p/18331/ Best, Ra ...
written 2.1 years ago by rkp2120
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Error while running cuffdiff "Fatal error: Exit Code 1()"
... Hello, I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18170/#18221). As those issues have been solved, I still have not had a successful cuffdiff run. I don't have any issues with alignment (HISAT) or with cufflinks. Now I am getting the error message below: ...
galaxy cufflinks software error rna-seq written 2.1 years ago by rkp2120 • updated 2.1 years ago by Jennifer Hillman Jackson25k
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Answer: A: Cuffquant errors after using HISAT2
... Hi, I had a similar error message as yours after using HISAT2, but I had skipped the cuffquant step and gone directly to cuffdiff. See here: https://biostar.usegalaxy.org/p/18170/ The solution to the XS tag problem is that you need to find an option in HISAT2 that says "report alignments specifica ...
written 2.1 years ago by rkp2120
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Comment: C: Cuffdiff Fatal error: Matched on error
... Hi Jen, Thanks for the reply. I initially tried this on a local galaxy instance, but was able to replicate the problem on usegalaxy.org as well. That being said I did my alignment with HISAT2 on my local galaxy instance and brought the BAM files and the Cuffmerge from my local galaxy instance dire ...
written 2.2 years ago by rkp2120
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Cuffdiff Fatal error: Matched on error
... Hello, I am doing my first RNA seq data analysis using galaxy. I have assembled my transcripts using Cufflinks and I merged my Cufflinks files using Cuffmerge. I am now trying to look at differential expression in the Cuffmerge .gtf output. I am trying to use Cuffdiff, but obtain the following erro ...
cufflinks galaxy software error rna-seq written 2.2 years ago by rkp2120 • updated 2.2 years ago by Jennifer Hillman Jackson25k

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Cuffquant errors after using HISAT2

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