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<prev • 47 results • page 1 of 2 • next >
4
votes
1
answer
131
views
1
answer
Big differences between mappings computed by Salmon and quantification
salmon rna-seq integrated genome viewer written 10 days ago by KDA • 20 • updated 7 days ago by Rob ♦ 2.4k
2
votes
2
answers
108
views
2
answers
Salmon choosing library type
alignment salmon written 24 days ago by bharata1803 • 280 • updated 24 days ago by igor ♦ 6.3k
1
vote
2
answers
100
views
2
answers
How can I produce gene level quantification using Salmon pseudo-aligner?
salmon rna-seq gene quantification written 28 days ago by Angelique • 10 • updated 27 days ago by stefanos.bamopoulos • 30
0
votes
1
answer
147
views
1
answer
Error with snakemake
python pipeline snakemake salmon written 5 weeks ago by Biologist • 60 • updated 5 weeks ago by WouterDeCoster ♦ 30k
0
votes
1
answer
102
views
1
answer
Salmon tool giving an error about the library type
salmon alignment rna rna-seq library written 8 weeks ago by Bioinfo • 220
2
votes
1
answer
107
views
1
answer
Genes' length to get RPKM if features count is not used?
rpkm salmon rna-seq edger written 9 weeks ago by Sharon • 340 • updated 9 weeks ago by h.mon ♦ 16k
0
votes
1
answer
179
views
1
answer
RNAseq Tximport transcript counts to gene counts
tximport salmon rna-seq written 11 weeks ago by s.kyungyong64 • 10 • updated 11 weeks ago by h.mon ♦ 16k
0
votes
0
answers
167
views
0
answers
How to add tdtomato to mouse genome for RNA seq analysis
salmon rna-seq written 3 months ago by jevanveen • 20
3
votes
1
answer
259
views
1
answer
Library type warning in Salmon
rnaseq salmon library-type written 3 months ago by grant.hovhannisyan • 900 • updated 3 months ago by Rob ♦ 2.4k
1
vote
0
answers
159
views
0
answers
Running salmon after subsetting the bam to transcripts annotated as protein coding in the GTF
gtf salmon samtools gencode written 3 months ago by rubic • 170
1
vote
1
answer
225
views
1
answer
How should effective lengths returned by Salmon be collapsed for Differential Expression?
alignment salmon rna-seq written 3 months ago by arf1389 • 10
0
votes
0
answers
189
views
0
answers
Salmon -- prepare reads
ngs transcriptomics salmon rna-seq written 5 months ago by afabian • 0
0
votes
1
answer
499
views
1
answer
Have Salmon output tabular files from Galaxy; need to import into R for DESeq2
salmon deseq2 tpm rna-seq written 7 months ago by Dennis • 0 • updated 7 months ago by WouterDeCoster ♦ 30k
1
vote
1
answer
354
views
1
answer
Salmon and reads order in fastq in quasi-mapping-based mode
salmon written 7 months ago by ZheFrench • 130 • updated 7 months ago by ATpoint • 5.7k
9
votes
2
answers
666
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5 follow
2
answers
Alignment dropped with Salmon
tophat salmon rna-seq written 8 months ago by Sharon • 340
3
votes
1
answer
493
views
1
answer
How low is too low mapping to proceed with differential expression analysis?
salmon mapping rna-seq written 8 months ago by Tania • 120 • updated 8 months ago by Devon Ryan ♦ 81k
4
votes
1
answer
556
views
1
answer
Salmon unmapped reads
salmon mapping rna-seq written 8 months ago by Sharon • 340 • updated 8 months ago by Sean Davis ♦ 24k
1
vote
0
answers
712
views
0
answers
Salmon very low mapping
salmon rna-seq written 8 months ago by Tania • 120
4
votes
1
answer
355
views
1
answer
How can we validate RNAseq differential gene expressions?
cuffdiff tophat salmon rna-seq edger written 8 months ago by Sharon • 340 • updated 8 months ago by Devon Ryan ♦ 81k
1
vote
0
answers
411
views
0
answers
Salmon, Getting New TPM from new, updated NumReads
numreads alignment salmon written 8 months ago by jjrin • 10
3
votes
1
answer
553
views
1
answer
Transcripts ID matching in tximport for edgeR
tximport salmon rna-seq edger written 8 months ago by Sharon • 340 • updated 8 months ago by WouterDeCoster ♦ 30k
4
votes
2
answers
663
views
2
answers
From transcripts counts of Salmon to genes counts needed by edgeR
salmon rna-seq edger written 8 months ago by Sharon • 340 • updated 8 months ago by Rob ♦ 2.4k
0
votes
1
answer
692
views
1
answer
DESeq2 design and batch effect
deseq2 salmon rna-seq batch effect written 9 months ago by georgewwp • 0
7
votes
2
answers
834
views
2
answers
error when run tximport for salmon files
quantification r error txtimport salmon rna-seq written 9 months ago by Lila M • 380
3
votes
1
answer
537
views
1
answer
which option is better for DESeq2 analysis: salmon or htseq-count?
htseq-count de salmon rna-seq written 9 months ago by Lila M • 380 • updated 9 months ago by kristoffer.vittingseerup • 470
2
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0
answers
482
views
0
answers
Any suggestions upon re-quantifying bam files downloaded from EBI-EGA archive with Salmon?
bedtools salmon samtools rna-seq written 10 months ago by vchris_ngs • 4.5k
0
votes
0
answers
380
views
0
answers
Salmon never completes, stuck on processing fragments
fastq salmon rna-seq written 10 months ago by jjrin • 10
5
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1
answer
416
views
1
answer
Salmon libType is required but missing, although I thought I supplied it
salmon rna-seq written 12 months ago by charlesmagnefr • 10
5
votes
1
answer
687
views
1
answer
SALMON's warning library type
salmon rna-seq written 13 months ago by biks.kestro • 10 • updated 13 months ago by WouterDeCoster ♦ 30k
3
votes
1
answer
661
views
1
answer
salmon, kallisto psuedoaligners are failing to process
aligners salmon kallisto rna-seq written 13 months ago by dr.prasad.bvls • 10 • updated 13 months ago by Rob ♦ 2.4k
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