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How to get counts for transcripts for all replicates

cuffdiff rna-seq fpkm cufflinks assembly written 5 days ago by j.m.fustin • 10

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bioconductor-cummerbund dependency will not resolve

cuffdiff local install conda cummerbund written 4 days ago by jkoral • 100 • updated 4 days ago by Jennifer Hillman Jackson ♦ 24k

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Cuffmerge GTF versus known annotation GTF used with Cuffdiff

cuffdiff cuffmerge cufflinks de rna-seq written 6 days ago by adoorprabha • 0 • updated 6 days ago by Jennifer Hillman Jackson ♦ 24k

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Recent Replies

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...
A: cummeRbund SQLite database error from Galaxy main CuffDiff tool by adoorprabha • 0
I am also having the similar problem as Vaisharaghu has posted.Please help as soon as possible.

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