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Enabling "GATK Advanced Options" on a tool impacts the run

indel realigner gatk galaxy options written 7 months ago by jgbaumann • 10 • updated 7 months ago by Jennifer Hillman Jackson ♦ 24k

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GATK indel realigner using custom reference

indel realigner custom reference gatk written 3.7 years ago by laura • 0 • updated 20 months ago by vignes.gangboard • 0

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Recent Replies

C: Running DESeq2 inside local Galaxy instance by Devon Ryan • 1.9k
Odd, I suspect that there was an error when creating the conda environment. You can try removing ...
A: why TopHat doesn't read my compressed dataset collection (Fastqsanger.gz)? -- D by Fat.eldefrawy • 0
Thank you, Jennifer. your suggestions helped me more
C: Where is Snippy? by sluro • 0
I was using the "main" UseGalaxy server. The European one has the tool. Thanks, Bjoern!
C: Barcode splitter error by Jennifer Hillman Jackson ♦ 24k
**UPDATE** This is a problem server side at Galaxy Main https://usegalaxy.org. An issue ticket h...
C: Help with an simple workflow (annotation)? by Jennifer Hillman Jackson ♦ 24k
Table Blast results are almost in the `interval` format. You will need to subtract 1 base from th...
C: Help with an simple workflow (annotation)? by vebaev • 130
As my thoughts are cleared, I need a way to convert a table blast result to GFF so I can intersec...
A: NG-CHM visulaization tab is not updating by Jennifer Hillman Jackson ♦ 24k
Hello, For troubleshooting help with the install, try contacting the tool authors. They will kno...
A: Help with an simple workflow (annotation)? by Jennifer Hillman Jackson ♦ 24k
Hello, Galaxy tutorials: https://galaxyproject.org/learn/ Public Galaxy sites, some of which ar...
A: ANOVA test for six time points having three replicates for each time point by Jennifer Hillman Jackson ♦ 24k
Hello, Try using **DeSeq2** within Galaxy. Tutorials with examples: https://galaxyproject.org/...
C: Star-Fusion last-matching gene pairs file by Jennifer Hillman Jackson ♦ 24k
Follow this ticket for updates: https://github.com/galaxyproject/usegalaxy-playbook/pull/107 Mea...
C: Running DESeq2 inside local Galaxy instance by jkoral • 100
Hi all, I have been working with Gina on this and we are using the latest version of Galaxy 18.01...
A: Running DESeq2 inside local Galaxy instance by jkoral • 100
Hi all, I have been working with Gina on this and we are using the latest version of Galaxy 18.01...

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