User: sekalazare

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sekalazare0
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Netherlands
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3 years, 3 months ago
Joined:
3 years, 4 months ago
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Posts by sekalazare

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Comment: A: can't upload data via FTP
... How do you mean you can't upload? Do the files show up and don't upload or do they not show up at all? What FTP server do you use? And are you using the main galaxy, usegalaxy.org? I upload my data to usegalaxy.org server using Cyberduck FTP application. I log into the server using the email and p ...
written 3.3 years ago by sekalazare0
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Error java.lang.OutOfMemoryError: Java heap space on GATK Count Covariates
... Hi all, I am trying to follow the recommended workflow for GATK SNP analysis on RNA-seq (https://www.broadinstitute.org/gatk/guide/topic?name=methods) on the Galaxy public server (usegalaxy.org). All is well until the count covariates step when I received this error: Picked up _JAVA_OPTIONS: -Dja ...
gatk count covariates java error snp analysis written 3.3 years ago by sekalazare0 • updated 3.3 years ago by Jennifer Hillman Jackson23k
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[bam_parse_region] fail to determine the sequence name
... I'm trying to run differential expression using EdgeR and/or DEseq2 on the Ratsch Lab galaxy server but I keep getting this error:   [bam_parse_region] fail to determine the sequence name   I mapped the groomed and filtered FastQ files with Tophat2 using the mm10 reference and did DE expression ...
bam genomes gtf identifiers rna-seq written 3.4 years ago by sekalazare0 • updated 3.4 years ago by Jennifer Hillman Jackson23k
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Cufflinks Assigning separate Cuff I.D. to gene that falls within location of known gene
... Hi, I am following the workflow for differential expression analysis using cuffdiff on galaxy as follows: Map with Tophat2 > Cufflinks of Bam using reference annotation as a guide > CuffMerge of cufflinks files > Cuffdiff using Bam + cuffmerge gtf. My reference annotation is UCSC genes.gt ...
cufflinks cuff id differential expression rna-seq written 3.4 years ago by sekalazare0 • updated 3.4 years ago by Jennifer Hillman Jackson23k

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