ballgown Posts

A: Conversion of a .vcf (variant control format) to a .maf (mutation annotation fil by Jennifer Hillman Jackson ♦ 24k
Hello, These tools have not been wrapped for Galaxy yet (at least not publically), but they coul...
C: Creating simple tool to downsample sam files, doesn't complete by mdgronke • 10
I'll check out the downsampling tool, thanks. We're migrating from Mobyle so at the moment I'm tr...
A: Creating simple tool to downsample sam files, doesn't complete by Jennifer Hillman Jackson ♦ 24k
Hello, There are a few choices: - Use the existing wrapped downsampling tool instead: https://...
C: GEO SRA fastq-dump with very low mapping rate (Galaxy) by Jennifer Hillman Jackson ♦ 24k
Great catch and followup! Thanks for posting back the info back here and for contacting GEO to fi...
C: Barcode splitter error "Can't locate Data/Dumper.pm" - ticketed issue, see answe by Jennifer Hillman Jackson ♦ 24k
**Confirmed:** The workaround is to use the tool at the **Galaxy Europe** mirror at https://usega...
A: STAR --winAnchorMultimapNmax parameter by Jennifer Hillman Jackson ♦ 24k
Hello, This option is left at the default (50) in the current Galaxy wrapped version of the tool...
A: Cufflinks C. elegans no gene names? by Jennifer Hillman Jackson ♦ 24k
Hello, The reference annotation must include the **tss_id, gene_id, and gene_name** attributes t...
A: DESeq2 Gene IDs by Jennifer Hillman Jackson ♦ 24k
Hello, Double check the annotation file that you are using versus the attributes being counted b...
A: Job Submission Failed by Jennifer Hillman Jackson ♦ 24k
Hello, There is likely a problem with the inputs. Please review the troubleshooting and tutorial...
A: Non-coding RNA feature type/attribute by Jennifer Hillman Jackson ♦ 24k
Hello, The "ID Attribute" is used by the tool to group together annotation lines. My guess is th...
A: How to covnvert gene id to gene names by Jennifer Hillman Jackson ♦ 24k
Hello, Double check your reference annotation file (GTF or GFF3). Make sure it has the attribute...
A: Compare 2 BAM files for covarage regions by Jennifer Hillman Jackson ♦ 24k
Hello, Please see the tools in the group **NGS: DeepTools**. Example usage is covered in these t...

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