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Differential Expression from Salmon Quant outputs without GTF/GFF3 annotation file
|
|
4
|
713
|
July 22, 2025
|
|
Differentially expressed genes
|
|
14
|
1210
|
November 11, 2022
|
|
mapping file - DESeq2 error
|
|
2
|
381
|
September 16, 2022
|
|
Implementing a command line tool with input and output folders as a Galaxy tool
|
|
2
|
481
|
July 22, 2025
|
|
salmonKallistoMtxTo10x not working
|
|
3
|
458
|
May 11, 2022
|
|
DESEQ2 error with filtered salmon-quant input
|
|
0
|
595
|
May 11, 2022
|
|
Does running Salmon in Galaxy output a mapping rate?
|
|
4
|
814
|
March 31, 2022
|
|
Calculating TPM from HISAT2 (bam) files
|
|
3
|
1674
|
March 7, 2022
|
|
Salmon output with transcript IDs
|
|
9
|
2003
|
December 21, 2023
|
|
Tximport in usegalaxy
|
|
3
|
498
|
October 13, 2022
|
|
salmon quantmerge giving fewer rows than expected
|
|
0
|
414
|
December 1, 2021
|
|
Salmon quantification using Ensembl references
|
|
4
|
1187
|
October 21, 2021
|
|
generate count matrix from salmon output in galaxy
|
|
1
|
604
|
October 8, 2021
|
|
Salmon: Index file and mapping of transcripts to genes
|
|
1
|
744
|
August 29, 2021
|
|
DESEQ2 results file empty (Galaxy)
|
|
7
|
893
|
August 9, 2021
|
|
Some tools can not be found by learning "Generating a single cell matrix using Alevin By: Wendi Bacon Jonathan Manning"
|
|
0
|
282
|
August 2, 2021
|
|
How to use the TPM data from either Stringtie or Sailfish or Killisto quant
|
|
7
|
1238
|
June 16, 2021
|
|
Unassigned Multimapping in featurecounts
|
|
9
|
10170
|
June 15, 2021
|
|
Salmon Quantmerge
|
|
1
|
954
|
May 21, 2021
|
|
What file to use for Deseq2 and where to get it from
|
|
3
|
690
|
March 19, 2021
|
|
errors when running Salmon data manager
|
|
0
|
635
|
March 18, 2021
|
|
Salmon Auxiliary files - mapping stats
|
|
1
|
416
|
March 4, 2021
|
|
Salmon quant to DESeq2
|
|
0
|
511
|
November 12, 2020
|
|
DEseq2 Error in read.table
|
|
4
|
1004
|
October 26, 2020
|
|
HISAT2 runs successfully with 76% alignment reported but empty BAM file (71 bytes)
|
|
8
|
1188
|
July 28, 2020
|
|
Salmon - Update request
|
|
3
|
843
|
June 29, 2020
|
|
Trinity align reads and estimate abundance Fatal Error
|
|
6
|
2098
|
December 21, 2023
|
|
What are the RNA-seq data processing steps in Galaxy according to de novo approach?
|
|
1
|
999
|
June 19, 2020
|
|
Question with Salmon quant and tximport
|
|
0
|
630
|
April 16, 2020
|
|
BAM files error with Salmon quant
|
|
1
|
901
|
April 2, 2020
|