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17 results • Page
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47
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18
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15 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 18 hours ago by
skdv2522
• 0 • written 5.5 years ago by
chparada
▴ 70
0
votes
2
replies
1.8k
views
CuffDiff hangs at same point
cufflinks
cuffdiff
RNA-Seq
updated 35 minutes ago by
chavanrenuka852
• 0 • written 8.3 years ago by
laboiss
• 0
0
votes
6
replies
1.5k
views
How to Convert Illumina Final Report File To Plink
Illumina
plink
updated 7 hours ago by
Yan
• 0 • written 13 months ago by
g744695539
• 0
1
vote
3
replies
1.1k
views
GraphAligner/vg surject - alignment output nonsense?
vg-toolkit
graphaligner
vg
vg-surject
vgteam
updated 9 hours ago by
stringsAsBaxters
• 0 • written 16 months ago by
Andrew
▴ 20
1
vote
15
replies
782
views
GTF file
cellranger-arc
GTF
cellranger-arc-2.0.2
updated 20 hours ago by
Juke34
8.6k • written 5 days ago by
IrK
▴ 80
5
votes
3
replies
268
views
How to represent arbitrarily length kmer?
kmer
12 hours ago by
dwpeng
▴ 20
2
votes
5
replies
219
views
No such variable: nextflow
nextflow
updated 10 hours ago by
Medhat
9.8k • written 1 day ago by
Mmar
• 0
4
votes
4
replies
186
views
If changing the RNA-Seq count normalisation method changes the DGE and downstream analysis results?
tpm
normalisation
fpm
13 hours ago by
analyst
▴ 50
0
votes
1
reply
144
views
Doublets in scRNAseq analysis
Doublet
scRNAseq
PBMC
updated 20 hours ago by
OmnibusX
▴ 80 • written 1 day ago by
Binghong
▴ 20
0
votes
1
reply
97
views
blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) databases
KEGG
KOG
blast
GO
updated 6 hours ago by
Mensur Dlakic
★ 28k • written 13 hours ago by
analyst
▴ 50
0
votes
1
reply
70
views
Script for Rstudio
Rstudio
Transcript
kallisto
analysis
updated 4 hours ago by
Mensur Dlakic
★ 28k • written 5 hours ago by
Pumla
• 0
0
votes
0
replies
66
views
Padjusted value = 1 in wilcox test
fdr
bulkrnaseq
wilcox
17 hours ago by
swathy
• 0
0
votes
0
replies
64
views
How can I Obtain hg38 cancer mutation and variation files
VCF
SNV
variation
mutation
13 hours ago by
kabir.deb
▴ 80
0
votes
0
replies
60
views
cuffdiff
stuck
cuffdiff
updated 10 hours ago by
Pierre Lindenbaum
163k • written 10 hours ago by
chavanrenuka852
• 0
0
votes
0
replies
49
views
Less stringent way of calling variants in PacBio data
bcftools
SNPs
variant
PacBio
10X
4 hours ago by
TheCatalyst
• 0
0
votes
0
replies
40
views
Classify SNPs from PacBio data
SNPs
PacBio
GEX
pigeon
10X
4 hours ago by
TheCatalyst
• 0
0
votes
0
replies
25
views
GSEA single cell
gsea
Scrna
2 hours ago by
SHP
• 0
17 results • Page
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Recent Votes
interpreting results from pathway analysis
A: What is the best way to rank genes for GSEA?
Answer: Generating consensus sequence from bam file
Answer: Generating consensus sequence from bam file
Comment: How to represent arbitrarily length kmer?
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
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★ 6.8k
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Comment: CuffDiff hangs at same point
by
chavanrenuka852
• 0
hi i have the same issue can you please provide me details how to create small ban file or how to provide subset of bams?
Comment: Script for Rstudio
by
Mensur Dlakic
★ 28k
I don't think anyone can help you until you tell us the error code.
Answer: blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) d
by
Mensur Dlakic
★ 28k
Don't know about GO and KEGG, but pretty sure there is no FASTA database for KOG. BLAST annotation is decidedly old-school, which I don't …
Comment: How to Convert Illumina Final Report File To Plink
by
Yan
• 0
Hi there, I have the same problem. did you success using SNPchimpRepo? Thanks!
Comment: GraphAligner/vg surject - alignment output nonsense?
by
stringsAsBaxters
• 0
Did you ever solve this? GraphAligner doesn't retain the base quality scores in the GAM output, see: https://github.com/maickrau/GraphA…
Comment: How to represent arbitrarily length kmer?
by
dwpeng
▴ 20
Hi, rob, thanks to your reply and I wrote a demo in Rust. Repo here: https://github.com/dwpeng/kmer
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
analyst
▴ 50
Okay thank you so much for making things clear. Raw counts were used for DGE analysis in DESeq2. Thanks a lot for saving time dsull!
Answer: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
dsull
★ 6.8k
OK, since you mention you're using DESeq2 for DGE analysis. DESeq2 uses counts (not FPKMs, not TPMs) for DGE. So if you're using DEseq2 co…
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
analyst
▴ 50
Thanks dsull, I am using deseq2 for DGE analysis
Comment: If changing the RNA-Seq count normalisation method changes the DGE and downstrea
by
dsull
★ 6.8k
How are you performing the DGE analysis / what tool are you using for it?
Comment: Generating consensus sequence from bam file
by
skdv2522
• 0
Can anyone tell me why there is NNNNNN= no of gaps present in the final fasta file while converting bam into fasta with samtools consensus …
Comment: Generating consensus sequence from bam file
by
skdv2522
• 0
After conversion i got multiple NNNNN in the final fasta file. can anyone tell be why this happens
Comment: How to represent arbitrarily length kmer?
by
dwpeng
▴ 20
Thank you for the detailed answer. I will read KMC' and cuttlefish's source code.
Comment: GTF file
by
Juke34
8.6k
Have you looked at this issue in GitHub https://github.com/10XGenomics/cellranger/issues/133 If we can catch the sorting issue I could sol…
Answer: Doublets in scRNAseq analysis
by
OmnibusX
▴ 80
I often see a small population of B cells expressing CD3D in scRNAseq data, and I also do find some papers discussing this phenomenon. I s…
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