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247 results • Page
2 of 5
Sort: Rank
Rank
Views
Votes
Replies
6
votes
7
replies
430
views
Trying to install Roary with Conda results in error message
roary
conda
updated 14 hours ago by
ATpoint
70k • written 1 day ago by
tobiwan
▴ 10
1
vote
3
replies
278
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 21 hours ago by
Basti
★ 1.4k • written 2 days ago by
Pegasus
▴ 80
2
votes
6
replies
616
views
Bad quality fastq files for analysis
quality
bad
DNA-seq
fastq
alignment
23 hours ago by
Gene_MMP8
▴ 220
11
votes
8
replies
603
views
How to perform synteny alignments and plots only with a gene?
Comparative
Evolution
Alignment
Synteny
Genomics
14 hours ago by
Rafael Soler
★ 1.1k
2
votes
5
replies
520
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 9 hours ago by
igor
13k • written 4 days ago by
e.r.zakiev
▴ 30
10
votes
21
replies
5.9k
views
12 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 6 hours ago by
Joana
• 0 • written 14 months ago by
ConvolutedGenome
▴ 10
0
votes
1
reply
342
views
Aproblem concerning methylation profiles of gene: how to add gene information below the BSmooth result?
BSmooth
methylation
R
DNA
15 hours ago by
diqixiaoyaoer
▴ 10
1
vote
3
replies
406
views
Filtering mitochondrion reads from FastQ files
fastq
mitochondrion
updated 15 hours ago by
Ram
38k • written 3 months ago by
javanokendo
▴ 20
0
votes
4
replies
384
views
seqret: command not found
seqret
updated 15 hours ago by
Ram
38k • written 5 months ago by
ÖZGÜN
• 0
1
vote
4
replies
344
views
Loading Traitdata file for WGCNA analysis
R
WGCNA
updated 13 hours ago by
Ram
38k • written 5 months ago by
priya.bmg
▴ 50
2
votes
2
replies
400
views
How to iterate through paired-end reads in pysam?
bam
sam
pysam
samtools
updated 15 hours ago by
Ram
38k • written 5 months ago by
zt10122
▴ 20
0
votes
1
reply
212
views
create BED file from whole genome index file
bed
awk
updated 13 hours ago by
Ram
38k • written 5 months ago by
Ranold Grijon
• 0
3
votes
3
replies
389
views
RNA sequencing bioinformatic analysis (CEL.gz file)
CEL
RNA-seq
updated 13 hours ago by
Ram
38k • written 5 months ago by
bioinformatics
▴ 10
0
votes
0
replies
375
views
Using infercnv R package
r
infercnv
Seurat
annotation
updated 13 hours ago by
Ram
38k • written 6 months ago by
j.jacob1
• 0
0
votes
8
replies
1.1k
views
How can i find longest sequence in fasta file on terminal
fasta
sequence
updated 13 hours ago by
Ram
38k • written 6 months ago by
logbio
▴ 30
0
votes
16
replies
1.4k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 11 hours ago by
Ram
38k • written 6 months ago by
yoser4
▴ 10
2
votes
12
replies
861
views
Generating vcf files per individual instead of one big file from bam files
vcf
bam
variant
updated 11 hours ago by
Ram
38k • written 7 months ago by
salman_96
▴ 70
0
votes
2
replies
328
views
Can't create index file of Bam file
bam
samtools
updated 11 hours ago by
Ram
38k • written 7 months ago by
Zahed Alam
• 0
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 11 hours ago by
Ram
38k • written 7 months ago by
Jacob
• 0
0
votes
11
replies
889
views
filtering multi sample vcf file
vcf
updated 11 hours ago by
Ram
38k • written 7 months ago by
Peerzada
• 0
0
votes
7
replies
1.1k
views
Convertion of FASTA file to FASTQ file
fasta
FASTQ
updated 11 hours ago by
Ram
38k • written 7 months ago by
sabreenaalam12345
• 0
0
votes
1
reply
280
views
Batch rename fasta file of RefSeq
fasta
refseq
updated 11 hours ago by
Ram
38k • written 7 months ago by
BATMAN
• 0
4
votes
2
replies
433
views
bioinformatic cost of whole genome sequencing
WGS
Whole-Genome-Sequencing
NGS
updated 15 hours ago by
Ram
38k • written 8 months ago by
Tohid
▴ 10
0
votes
0
replies
188
views
PSL file confusion on negative strand
BLAT
PSL
updated 11 hours ago by
Ram
38k • written 8 months ago by
spark
• 0
0
votes
0
replies
187
views
Comparing PopoolationTE2 output with reference .bed file in Python
bed
python
pandas
PopoolationTE2
updated 11 hours ago by
Ram
38k • written 8 months ago by
Emilia
• 0
0
votes
2
replies
374
views
Which database should I get variant data from WGS for Asian and AA populations
vcf
WGS
variant
database
updated 11 hours ago by
Ram
38k • written 8 months ago by
minghuiguo448
• 0
4
votes
13
replies
910
views
6 follow
select rows in a tab-delimited ed file
linux
text
updated 11 hours ago by
Ram
38k • written 8 months ago by
S.O.T.AL-HASHIMI2
▴ 40
0
votes
0
replies
275
views
SURVIVOR bed file
BED
CNV
SURVIVOR
VCF
updated 11 hours ago by
Ram
38k • written 8 months ago by
Nameless
• 0
4
votes
12
replies
1.1k
views
What is the command to download GTF from NCBI
ncbi
gtf
linux
updated 11 hours ago by
Ram
38k • written 8 months ago by
smithkthedale
▴ 10
0
votes
3
replies
397
views
splitting a bam file by XA tag into multiple lines
bam
BWA
updated 11 hours ago by
Ram
38k • written 9 months ago by
eric.londin
▴ 50
1
vote
2
replies
278
views
Failed quality score and sequence content small RNA-seq data
quality
fasta
FastQC
updated 11 hours ago by
Ram
38k • written 9 months ago by
Rey
• 0
0
votes
3
replies
369
views
Annovar file to maf file conversion
maf
R
annovar
updated 11 hours ago by
Ram
38k • written 9 months ago by
ganeshram
• 0
0
votes
0
replies
170
views
Save Scene File in PDB in YASARA
YASARA
SCENE
PDB
updated 11 hours ago by
Ram
38k • written 9 months ago by
misbahnaseem95
• 0
2
votes
2
replies
496
views
Could bowtie2 use a fasta file as input to be mapped against a reference genome?
BAM
bowtie2
updated 11 hours ago by
Ram
38k • written 9 months ago by
andrea.aguado.marin
• 0
0
votes
0
replies
187
views
How to convert .bed/.bim/.fam file to .dat file to run --dosage command to get INFO
plink
dosage
updated 11 hours ago by
Ram
38k • written 9 months ago by
Raju
• 0
0
votes
2
replies
394
views
bwa error
index
bwa
updated 11 hours ago by
Ram
38k • written 9 months ago by
amahdi779
• 0
1
vote
1
reply
376
views
LFTP fails to submit files to the EGA sequence database
lftp
EGA
updated 10 hours ago by
Ram
38k • written 10 months ago by
heskett
▴ 100
0
votes
2
replies
399
views
How to remove evidence tags and unnecessary information in the uniprot tab file
UNIPROT
updated 10 hours ago by
Ram
38k • written 10 months ago by
devhimd
▴ 10
0
votes
3
replies
425
views
GC @5,20,50 : Fraction of GC content in the bases around the variant position
fasta
genome
GC-content
updated 10 hours ago by
Ram
38k • written 10 months ago by
Maryem
▴ 10
0
votes
1
reply
329
views
I have two different libaries which were sequenced, How should I compare their library diversity?
bam
sam
updated 15 hours ago by
Ram
38k • written 10 months ago by
zt10122
▴ 20
2
votes
4
replies
559
views
What's the difference between library diversity and unique molecules?
bam
sam
updated 15 hours ago by
Ram
38k • written 10 months ago by
zt10122
▴ 20
0
votes
0
replies
156
views
How to generate a bed file indicating increased ratio of H3K4me3 to H3K4me1
H3K4me3
bed
H3K4me1
updated 10 hours ago by
Ram
38k • written 10 months ago by
jia
• 0
0
votes
0
replies
163
views
MEME motif discovery
fasta
updated 10 hours ago by
Ram
38k • written 10 months ago by
kaisakaiho73847
• 0
1
vote
1
reply
453
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 10 hours ago by
Ram
38k • written 10 months ago by
ManuelDB
▴ 30
0
votes
5
replies
485
views
BAM file became smaller after merging
BAM
updated 10 hours ago by
Ram
38k • written 10 months ago by
kimmitzka
• 0
2
votes
4
replies
620
views
Why the bed file not recognized as a bed file
peak
bed
updated 10 hours ago by
Ram
38k • written 11 months ago by
brgs
• 0
2
votes
3
replies
496
views
Featurecounts
featurecounts
bam
RNA-seq
updated 10 hours ago by
Ram
38k • written 11 months ago by
edus_bioinfo
▴ 20
3
votes
1
reply
256
views
String of 'N's at same location in Fasta file
fasta
sequence
updated 10 hours ago by
Ram
38k • written 11 months ago by
zdiazmar
▴ 20
0
votes
2
replies
573
views
GROMACS error
gromacs
topology
updated 9 hours ago by
Ram
38k • written 11 months ago by
ali.kian.saei
▴ 10
0
votes
0
replies
225
views
Tapestry scDNA-seq and translocations
scDNA-seq
H5
single-cell
MOSAIC
variant-calling
updated 9 hours ago by
Ram
38k • written 11 months ago by
jmnz22
• 0
247 results • Page
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Answer: RNA-SEQ
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Answer: RNA-SEQ
Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Recent Replies
Comment: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
![enter image description here][1] enter image description here ![enter image description here][2] [1]: /media/images/d06e761c-b715…
Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Ruben
• 0
> Unfortunately, as far as I can tell, WDL provides no support for iterating over the contents of a directory. (I find this shocking. I con…
Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial suppli…
Comment: RNA-SEQ
by
ali
• 0
thanks for your helping
Comment: TSS of protein coding genes
by
ConvolutedGenome
▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da
by
iraun
5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
Andy
• 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39
by
seidel
11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard
by
ntsopoul
▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
thank you. i will go through it
Comment: Fastqc report analysis
by
npavliukovec
• 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number
by
kimgeng
• 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number
by
ntsopoul
▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
Answer: Can I use abundance from Tximport to compare the expression level of transcript
by
ntsopoul
▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
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