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95 results • Page
2 of 2
Sort: replies
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Views
Votes
Replies
0
votes
1
reply
303
views
Assign RSID to ID . / blank column in vcf file
ID
VCF
updated 20 hours ago by
Ram
38k • written 13 months ago by
Nai
▴ 50
0
votes
1
reply
25
views
Is there a site that takes a list of uniprot IDs/gene IDs as input and create phylogenetic tree?
phylogenetictree
updated 58 minutes ago by
Pierre Lindenbaum
153k • written 1 hour ago by
Diwan
▴ 650
0
votes
1
reply
172
views
pyscenic
pyscenic
scenic
2 hours ago by
Andy
▴ 30
0
votes
1
reply
118
views
Error when using compareCluster from enichment
compareCluster
updated 9 hours ago by
Basti
★ 1.4k • written 1 day ago by
jacob
• 0
1
vote
1
reply
69
views
RNAseq: same reads + more complete scaffold = fewer DEGs?
RNAseq
updated 5 hours ago by
Darked89
4.2k • written 6 hours ago by
phillip.brassington
▴ 10
0
votes
1
reply
282
views
Batch rename fasta file of RefSeq
fasta
refseq
updated 22 hours ago by
Ram
38k • written 7 months ago by
BATMAN
• 0
1
vote
1
reply
525
views
CNV in EPIC Illumina DNA methylation
bed
CNV
Conumee
updated 1 hour ago by
Ram
38k • written 21 months ago by
NS
• 0
0
votes
1
reply
279
views
exome targeted regions ensembl
bed
exome
updated 20 hours ago by
Ram
38k • written 12 months ago by
mailard
▴ 10
0
votes
1
reply
671
views
map file for BEAGLE imputation
beagleV5.2
Impute
BEAGLE
updated 2 hours ago by
Ram
38k • written 16 months ago by
rachael.kane
• 0
0
votes
1
reply
363
views
RefSeq obtained from genome.ucsc.edu
Genome-browser
Annotation
sequence
updated 7 minutes ago by
Ram
38k • written 22 months ago by
Apex92
▴ 260
0
votes
1
reply
31
views
Manta and alignment name collision
SV
updated 41 minutes ago by
Pierre Lindenbaum
153k • written 3 hours ago by
German.M.Demidov
★ 2.9k
0
votes
1
reply
446
views
How to select dataset from 1000 genome
1000genomes
vcf
updated 1 hour ago by
Ram
38k • written 19 months ago by
pragnapcu
• 0
0
votes
0
replies
1.5k
views
linkage disequilibrium of snps using plink
ped
linkage-disequilibrium
SNP
plink
map
updated just now by
Ram
38k • written 5.0 years ago by
14311a2301
• 0
0
votes
0
replies
172
views
Save Scene File in PDB in YASARA
YASARA
SCENE
PDB
updated 22 hours ago by
Ram
38k • written 9 months ago by
misbahnaseem95
• 0
0
votes
0
replies
506
views
Error in genetics vcf file - !! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..
vcf
genetics
updated 20 hours ago by
Ram
38k • written 15 months ago by
Nance
• 0
0
votes
0
replies
191
views
PSL file confusion on negative strand
BLAT
PSL
updated 22 hours ago by
Ram
38k • written 8 months ago by
spark
• 0
0
votes
0
replies
369
views
lncRNA-target reference file with proper gene nomenclature
gene
genome-sequencing
lincRNA
updated 6 minutes ago by
Ram
38k • written 2.0 years ago by
Apex92
▴ 260
0
votes
0
replies
292
views
Isaac aligner with unmapped reads in BAM file
BAM
updated 1 hour ago by
Ram
38k • written 19 months ago by
OMG_HG
• 0
0
votes
0
replies
11
views
pyscenic feather file
pyscenic
1 hour ago by
Andy
▴ 30
0
votes
0
replies
51
views
Hi-C aggregation plot | ARA | PE-Scan
Hi-C
6 hours ago by
Argonaut
• 0
0
votes
0
replies
229
views
Tapestry scDNA-seq and translocations
scDNA-seq
H5
single-cell
MOSAIC
variant-calling
updated 20 hours ago by
Ram
38k • written 11 months ago by
jmnz22
• 0
0
votes
0
replies
13
views
How to bifurcate patients into high and low expressing groups for TCGA survival analysis for a gene of interest
Meidan
TCGA
Percentile
Survival
R
1 hour ago by
Manav
• 0
0
votes
0
replies
33
views
Outgroup for plastome NJ-tree (from pseudoalignment based on SNPs)
bwa-mem2
samtools
freebayes
mega
vcf2phylip
4 hours ago by
poecile.pal
▴ 50
0
votes
0
replies
9
views
how to get the nucleotide squence behind a symbolic ALT in VCF
SV
vcf
sniffles
30 minutes ago by
Maxine
• 0
0
votes
0
replies
9
views
How can I retrive the actual amino acid and the alternative amino acid (if any cordon changes happened due to editing)?
RNA
editing
40 minutes ago by
Genetics
▴ 20
0
votes
0
replies
165
views
MEME motif discovery
fasta
updated 20 hours ago by
Ram
38k • written 10 months ago by
kaisakaiho73847
• 0
0
votes
0
replies
409
views
getting bed files into R
bed
R
Plink
updated 3 minutes ago by
Ram
38k • written 2.8 years ago by
wrab425
▴ 40
0
votes
0
replies
279
views
How to use PhyloCSF
non-coding-RNA
annotation
updated 36 minutes ago by
Ram
38k • written 14 months ago by
Nobody
▴ 30
0
votes
0
replies
79
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
15 hours ago by
rheab1230
▴ 140
0
votes
0
replies
672
views
how to calculate genetic position for each marker from the genetic map file?
genetic-position
map
updated just now by
Ram
38k • written 3.9 years ago by
Ana
▴ 200
0
votes
0
replies
1.3k
views
How to check consistency of data sets and 1000G reference panel?
plink
immunochip
updated just now by
Ram
38k • written 6.5 years ago by
fatima
▴ 20
0
votes
0
replies
366
views
how to match row names of two files quickly using python
python
pandas
updated 9 minutes ago by
Ram
38k • written 22 months ago by
szp770
▴ 10
0
votes
0
replies
456
views
How to plot heatmap for the matrix for the pairwise comparison of sequence similarity in python?
heatmap
python
distance-matrix
updated 20 hours ago by
Ram
38k • written 15 months ago by
ramsha
• 0
0
votes
0
replies
278
views
SURVIVOR bed file
BED
CNV
SURVIVOR
VCF
updated 22 hours ago by
Ram
38k • written 8 months ago by
Nameless
• 0
0
votes
0
replies
47
views
Spearman correlation rna-seq gene to blood values
spearman
rna-seq
updated 4 hours ago by
Hemal
• 0 • written 4 hours ago by
bas2020
• 0
0
votes
0
replies
191
views
Comparing PopoolationTE2 output with reference .bed file in Python
bed
python
pandas
PopoolationTE2
updated 22 hours ago by
Ram
38k • written 8 months ago by
Emilia
• 0
0
votes
0
replies
57
views
displaying results of different RNA-seq projects in R shiny
RNA-seq
shiny
R
5 hours ago by
rls_08
▴ 40
0
votes
0
replies
219
views
Merging Sample in vcf file having SNPs info
VCF
updated 20 hours ago by
Ram
38k • written 11 months ago by
amar.kant20422
• 0
0
votes
0
replies
290
views
Fetch rsid and related genotype/sample from vcf file
vcf
rsid
updated 2 hours ago by
Ram
38k • written 17 months ago by
Nai
▴ 50
0
votes
0
replies
159
views
How to generate a bed file indicating increased ratio of H3K4me3 to H3K4me1
H3K4me3
bed
H3K4me1
updated 20 hours ago by
Ram
38k • written 10 months ago by
jia
• 0
0
votes
0
replies
46
views
calc IBS with vcf files
IBS
PLINK
6 hours ago by
Mali
• 0
0
votes
0
replies
190
views
How to convert .bed/.bim/.fam file to .dat file to run --dosage command to get INFO
plink
dosage
updated 22 hours ago by
Ram
38k • written 9 months ago by
Raju
• 0
0
votes
0
replies
12
views
Something wrong with my code concerning bsseq visualization
bsseq
plotRegion
R
1 hour ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
320
views
predixcan error
vcf
predixcan
updated 2 hours ago by
Ram
38k • written 18 months ago by
rheab1230
▴ 140
0
votes
0
replies
183
views
Diffbind output file default contrasts
Diffbind
updated 20 hours ago by
Ram
38k • written 13 months ago by
c.eskiw
▴ 10
95 results • Page
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Hello! There are two questions here: 1) Mixed species, and 2) Multiple samples Let's start with question 1: You don't really know what c…
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I dont think im confusing the two, is what I meant: I originally said that the “start” coordinate of every entry termed “transcript” under…
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Your account has been suspended for bad behavior. I've re-opened the posts that you deleted because those posts belong to the community, no…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
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38k
No. I think you can compare average TPMs as long as you explicitly mention that anywhere you report metrics but don't average counts.
Comment: Manta and alignment name collision
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153k
I wrote https://jvarkit.readthedocs.io/en/latest/SamRemoveDuplicatedNames/ to remove this kind of reads, but I'm not sure it's what you're …
Comment: getting coding exon information from Ensembl API
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Nobody
▴ 30
can you delete my account please, because i can't do it by myself. Thank you
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twrl8
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Thank you very much! I will try using the singularity options. Thank you for that aswell. I will keep an eye on the docker hub for newer v…
Comment: Is there a site that takes a list of uniprot IDs/gene IDs as input and create ph
by
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153k
ncbi blast a sequence accession vs the other ? then select the multiple sequence alignment view ?
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
So can I average 6 replicates??
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
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7.7k
Don't use `--merge_loci` in your command line this was for AGAT version <1.0.0 (and only few scripts), now this is handled via the config.y…
Comment: getting coding exon information from Ensembl API
by
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38k
> Because you just answer No we don't. I think you're confusing this professional forum contributed to by volunteers with a customer suppo…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
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38k
Oh, you can just use TPM to do that. Within sample comparison is a completely different (and much easier) game.
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Unfortunately yes, there does seem to be a problem with using the older version - when I came to do more analysis yesterday, the enrichKEGG…
Comment: getting coding exon information from Ensembl API
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Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
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Thanks, tried working with the dataset and workflow. It worked.
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