User: federico.bernuzzi

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20
Status:
New User
Location:
Quadram Institute of BioSciences
Last seen:
2 months, 1 week ago
Joined:
8 months ago
Email:
f****************@gmail.com

Posts by federico.bernuzzi

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Free Bayes Exit code error
... Thanks Jen, much appreciated ...
written 11 weeks ago by federico.bernuzzi20
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Free Bayes Exit code error
... Hi guys Has anyone come across this error? Fatal error: Exit code 25 () unable to find FASTA index entry for '10' unable to find FASTA index entry for '1' unable to find FASTA index entry for '11' unable to find FASTA index entry for '12' unable to find FASTA index entry for '13' unable to find FA ...
bam galaxy software error rna-seq written 11 weeks ago by federico.bernuzzi20 • updated 11 weeks ago by Jennifer Hillman Jackson23k
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Answer: A: SnpEff output searching for specific genes
... Many thanks for the reply I shall look into it. ...
written 6 months ago by federico.bernuzzi20
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SnpEff output searching for specific genes
... Hi, I have successfully runned SnpEff. The ouput VCF file contains 2.5 million "lines", data sets. I wanted to ask if someone is interested in looking at only a couple of genes how would I go about doing this? In addition is there a chance than the output VCF file can be transported into a differen ...
galaxy snp rna-seq written 6 months ago by federico.bernuzzi20 • updated 6 months ago by Guy Reeves1.0k
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Answer: A: SnpEff Error linked to inputs chromosome mismatches
... Hi Jen, Many thanks for the reply. Yes you are correct that the problem is a mismatch. I went to the SnpEff documentation page and what the error means is that the input VCF file has chromosome names that do not match SnpEff's database and don't match reference genome either, since SnpEff's databas ...
written 7 months ago by federico.bernuzzi20
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SnpEff Error linked to inputs chromosome mismatches
... Dear all, I have runned SnpEff, it seems to have worked and whilst looking through the results for a lot of the readings I get the following output, which I presume its not correct? EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND) Any advice on what the error implies? Many thanks ...
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Comment: C: Error message after running FreeBayes
... Hi Anton, You raised a very good point. I thought that maybe HISAT2 might cause the problem and was thinking of running TopHat and then putting the results (the accepted hits file) into FreeBayes to see whether that would work. I have not come across Naive Variant Caller so I am not exactly sure ho ...
written 8 months ago by federico.bernuzzi20
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Answer: A: Error message after running FreeBayes
... Hi Jen, Many thanks for the advice and help Kind regards FB ...
written 8 months ago by federico.bernuzzi20
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Error message after running FreeBayes
... Hi, I am quite new with Galaxy only been working with it for a month so please bare with me. I am trying to identify SNP variants from RNA-Seq data of prostate cancer tissue. All of the previous steps in the pipeline have successfully worked (FastQC, TrimGalore, FASTQC and HISAT2). When i launch Fr ...
rna-seq galaxy software error snp written 8 months ago by federico.bernuzzi20 • updated 8 months ago by Anton Nekrutenko1.7k

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