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22 results • Page
1 of 1
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Votes
Replies
0
votes
10
replies
242
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
10 minutes ago by
atowns21
• 0
2
votes
9
replies
709
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
4
replies
180
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 12 hours ago by
GenoMax
141k • written 14 hours ago by
njornet
▴ 20
2
votes
3
replies
186
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 17 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
1
vote
3
replies
160
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
16 hours ago by
WouterDeCoster
47k
0
votes
3
replies
152
views
some error in building kraken2 database
metagenome
kraken2
1 hour ago by
Art1ess
• 0
0
votes
2
replies
155
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 5 hours ago by
Istvan Albert
100k • written 21 hours ago by
qudrat.nii
▴ 10
0
votes
1
reply
71
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 4 hours ago by
GenoMax
141k • written 6 hours ago by
v.berriosfarias
▴ 140
0
votes
1
reply
95
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 12 hours ago by
bk11
★ 2.3k • written 18 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
70
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 9 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
Lada
▴ 30
0
votes
1
reply
83
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 8 hours ago by
bk11
★ 2.3k • written 8 hours ago by
alphaflylizard
• 0
1
vote
1
reply
127
views
Failed kmer content
kmer
illumina
ngs
updated 12 hours ago by
Ram
43k • written 20 hours ago by
Kasturi
• 0
0
votes
1
reply
91
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 14 hours ago by
GenoMax
141k • written 14 hours ago by
Srinka
▴ 20
0
votes
0
replies
61
views
Merging replicates from Encode project
CHIP-seq
encode
15 hours ago by
Nurken
• 0
0
votes
0
replies
66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
16 hours ago by
alifafiq1
• 0
0
votes
0
replies
38
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
5 hours ago by
benguyarenbeyaz98
• 0
0
votes
0
replies
83
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 12 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
48
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
11 hours ago by
ohtang7
▴ 40
0
votes
0
replies
63
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 11 hours ago by
Ram
43k • written 23 hours ago by
SSSJec
• 0
0
votes
0
replies
54
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 12 hours ago by
Ram
43k • written 15 hours ago by
SHREYA
• 0
0
votes
0
replies
32
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
4 hours ago by
mropri
▴ 150
0
votes
0
replies
31
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
4 hours ago by
Kash
▴ 110
22 results • Page
1 of 1
Recent Votes
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
Comment: Bwa sampe - BGI
Comment: Redirection of Duplicate PMIDs
Answer: Redirection of Duplicate PMIDs
A: Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To
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Recent Awards •
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Popular Question
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▴ 140
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AdviceSeeker
• 0
Great Question
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★ 2.4k
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marco.barr
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Recent Replies
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 360
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Yes, that is a very good idea. Thanks for the help!
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
Only thing would be to try them out. See if you can detect them in the data you have. You could also simply look for unique representativ…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
GenoMax
141k
`clustal omega` can calculate distance matrix between two proteins (makes sense if your proteins are of similar size). You could try that: …
Comment: Should I use unpaired reads from trimmomatic
by
swbarnes2
14k
If the unpaired are _2, files, the _1 must exist somewhere. But the simple answer is probably going to be to just use all the _2 only. Yo…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
GenoMax
141k
> The needless granularity (fake precision) was obvious from the start You are assuming that all data generated is always of great quality…
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