User: Joan Gibert

gravatar for Joan Gibert
Joan Gibert20
Reputation:
20
Status:
New User
Location:
Barcelona/PRBB
Last seen:
2 months, 2 weeks ago
Joined:
1 year, 8 months ago
Email:
j***********@gmail.com

Posts by Joan Gibert

<prev • 9 results • page 1 of 1 • next >
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Comment: C: BAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38) - d
... Hi Jen! Thank you for the great answer! I supposed that change the header would be a difficult task, I'm on a hurry right now so I guess that I will skip the steps which require header comparisons. A pity that nobody scripted anything about changing headers/names on this different hg38 reference ...
written 11 weeks ago by Joan Gibert20
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BAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38) - deprecated tools in Galaxy
... Hi! I am trying to perform some analysis using GATK in order to identify mutations. Long sotry short, I performed BWA-MEM using hg38 in Galaxy and now I'm using hg38 provided in the GATK resource bundle (https://software.broadinstitute.org/gatk/download/bundle). The problem is that the header for t ...
deprecated gatk snp bwa alignment written 11 weeks ago by Joan Gibert20 • updated 11 weeks ago by Jennifer Hillman Jackson25k
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Realigner Target Creator (GATK) with a custom or native local genome
... Hi! I cannot introduce any local reference genome in the Realigner Target Creator. Is this because is beta? Thanks! Joan ...
freebayes custom gatk genome snp written 3 months ago by Joan Gibert20 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: HISAT2 and custom reference genome
... Thanks for the information! However, I have couple of issues... First, you comment that HISAT2 mapping worked but when I tried to check the reads in UCSC browser, nothing appears. Is there any manipulation that I should perform to the sample to see it in the browser? I will fight a bit with the ide ...
written 9 months ago by Joan Gibert20
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Answer: A: HISAT2 and custom reference genome
... Hello Jen! I performed a HISAT aligment with a 3'UTR genome (using NormalizeFasta output) in the "main" Galaxy server, for you to check. It appeared again the code that I wrote in the previous post, but it does not seem an error to me. I guess that it is a kind of error... Anyway, my idea after th ...
written 9 months ago by Joan Gibert20
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HISAT2 and custom reference genome
... Hi! I want to perform HISAT2 aligment in galaxy using a custom genome. In this case I want to use 3'UTR genome from hg38. I obtain it from Table Browser by generating a custom track with 3'UTR of the hg38 and sending the custom track to Galaxy in fasta format. When I run HISAT2 in Galaxy, it didn' ...
rna-seq written 9 months ago by Joan Gibert20
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Comment: A: Deseq2 RIP seq analisys
... Here it is the full error: Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row. ...
written 20 months ago by Joan Gibert20
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Comment: C: Deseq2 RIP seq analisys
... Hi! I'm using the Galaxy Main http://usegalaxy,org ...
written 20 months ago by Joan Gibert20
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Deseq2 RIP seq analisys
... I am following this: https://support.bioconductor.org/p/61509/ After HTseq, Deseq2 cannot perform the (IP for B / IP for A) / (Input for B / Input for A). I did this by adding two different "Factors". The first with the RIPseq data (1st Factor level WT; 2nd Factor level KO) and the second the RNAse ...
deseq2 written 20 months ago by Joan Gibert20 • updated 20 months ago by Jennifer Hillman Jackson25k

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