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Limit : this year
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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Shahzad
▴ 30
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 10 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 6 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
7
votes
8
replies
8.9k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
4
votes
12
replies
7.7k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 10 weeks ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
2
votes
9
replies
7.5k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 4 months ago by
GenoMax
141k • written 6.0 years ago by
ft821525
• 0
0
votes
7
replies
7.2k
views
Problem in in alignment by muscle
sequence
muscle
alignment
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 12 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
6
votes
4
replies
6.5k
views
What is gnomAD allele frequency
AF
gnomAD
updated 3 months ago by
Lhl
▴ 760 • written 3.0 years ago by
Eric Wang
▴ 50
3
votes
7
replies
6.3k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 10 months ago by
DareDevil
★ 4.3k • written 6.2 years ago by
win
▴ 970
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly
Trinity
RNA-seq
trimmomatic
updated 10 months ago by
Ram
43k • written 8.1 years ago by
lay_0
▴ 50
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 6 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 6 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
2
votes
14
replies
5.9k
views
Using sam-dump in SRA toolkit to download chr20.bam from NA12878
sratoolkit
sam-dump
updated 10 months ago by
Ram
43k • written 7.0 years ago by
Covux
▴ 10
3
votes
14
replies
5.9k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
updated 3 months ago by
K.Gee
▴ 40 • written 3.1 years ago by
janneken0210
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 3 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
4
replies
5.9k
views
using IGV to visualize RNA seq alignment to transcriptome
rna-seq
igv
alignment
updated 8 months ago by
Ram
43k • written 7.9 years ago by
nikelle.petrillo
▴ 110
1
vote
5
replies
5.8k
views
Generate VCF File from Bam file and fasta by GATK
vcf
SNP
genome
next-gen
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
0
votes
3
replies
5.6k
views
Bedgraphtobigwig Conversion Difficulties
bigwig
updated 9 months ago by
Ram
43k • written 11.2 years ago by
stu.andrews
• 0
1
vote
4
replies
5.5k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 11 months ago by
Ram
43k • written 6.1 years ago by
chetana
▴ 60
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq
rna-seq
htseq
FPKM
TPM
updated 8 months ago by
ATpoint
81k • written 5.0 years ago by
Joel Wallenius
▴ 210
0
votes
1
reply
5.3k
views
Hapmap to vcf
vcf
hapmap
updated 9 months ago by
Ram
43k • written 5.6 years ago by
shinken123
▴ 150
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 13 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
4
replies
5.3k
views
Sequence alignment length
multiple-sequence-alignment
updated 11 months ago by
Ram
43k • written 7.2 years ago by
biobudhan
▴ 20
2
votes
11
replies
5.2k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 3 months ago by
e.r.zakiev
▴ 200 • written 7.8 years ago by
CAnna
▴ 20
3
votes
4
replies
5.2k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 9 months ago by
tirza.doniger
▴ 10 • written 8.7 years ago by
tiago211287
★ 1.4k
7
votes
7
replies
4.9k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.3 years ago by
stu111538
▴ 80
10
votes
14
replies
4.9k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 10 months ago by
Ram
43k • written 4.2 years ago by
gable_works
▴ 50
1
vote
4
replies
4.8k
views
TCGA data(RPKM) differential gene expression
rna-seq
R
TCGA
RPKM
IPA
9 months ago by
realnewbie
▴ 30
3
votes
2
replies
4.7k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 8 months ago by
logbio
▴ 30 • written 4.4 years ago by
The
▴ 180
2
votes
7
replies
4.6k
views
SRA toolkit internet settings
sratoolkit
fastq-dump
sequencing
RNA-Seq
updated 10 months ago by
Ram
43k • written 7.7 years ago by
BCArg
▴ 90
0
votes
8
replies
4.4k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 8 months ago by
Ram
43k • written 5.3 years ago by
V
▴ 380
0
votes
7
replies
4.4k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq
alignment
software-error
next-gen
sequence
updated 4 months ago by
Ram
43k • written 5.9 years ago by
nasreenbano91
• 0
1
vote
0
replies
4.4k
views
how to convert .geno/.snp/.ind to .bed/.bim/.fam (ped plink format) in Windows
plink
genomes
ancestrymap
updated 9 months ago by
Ram
43k • written 7.8 years ago by
Ghoul
▴ 10
3
votes
4
replies
4.4k
views
Atypical volcano plot RNA-seq
volcano-plot
RNA-seq
deseq2
updated 8 months ago by
Ram
43k • written 5.5 years ago by
Teresa
▴ 20
7
votes
13
replies
4.4k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq
trimming
fastqc
updated 5 months ago by
ATpoint
81k • written 3.4 years ago by
Pac314
▴ 10
1
vote
9
replies
4.3k
views
Unable to install bioconda and bowtie
bioconda
conda
updated 4 months ago by
rpolicastro
13k • written 19 months ago by
n.anuragsharma
▴ 30
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 10 months ago by
Ram
43k • written 3.9 years ago by
kand3e
▴ 60
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 13 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 4 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 11 months ago by
Ram
43k • written 6.2 years ago by
scottschu97
▴ 20
0
votes
4
replies
4.1k
views
What is Dunn's multiple comparison test?
statistics
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Koreanraichu
• 0
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 13 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
1
vote
7
replies
4.0k
views
Adjust width of annotations in pheatmap
R
heatmap
updated 6 months ago by
Kevin Blighe
87k • written 5.5 years ago by
divya.nandakumar
▴ 30
2
votes
4
replies
4.0k
views
Transcriptomic Coordinate Bam To Genomic Coordinate Bam
bam
genomics
updated 9 months ago by
Ram
43k • written 11.3 years ago by
Ge
▴ 80
1
vote
5
replies
4.0k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 10 months ago by
Ram
43k • written 7.6 years ago by
Biogeek
▴ 470
5
votes
19
replies
4.0k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.9 years ago by
ta_awwad
▴ 340
0
votes
5
replies
3.9k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 11 months ago by
Ram
43k • written 5.1 years ago by
marina.gerges
• 0
1
vote
8
replies
3.9k
views
No gene can be mapped
R
GSEA
updated 4 months ago by
jv
★ 1.8k • written 2.3 years ago by
yang.zhizhang
• 0
1,000 results • Page
1 of 20
Recent Votes
The Biostar Herald for Monday, April 15, 2024
The Biostar Herald for Monday, April 15, 2024
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Fast way to extract specific sequences from large fasta
Answer: Fast way to extract specific sequences from large fasta
Comment: Intersect multiple BED files
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Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
Answer: Using vg gamsort with naive sorting algorithm
by
anovak
▴ 110
The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file. To fin…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
Comment: Plot DNA methylation level of DMR on the basis of certain genes
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
Yes you can remove those if you are only interested in annotated genes.
Comment: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
[This could help][1] [1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
Answer: How to compare the quality of assemblies
by
colindaven
6.4k
Are you sure you have looked into the HiFiasm output files (fasta and GFA) in detail and excluded non-primary contigs, hap1, hap2 and other…
Answer: How to identify gaps in a genome?
by
colindaven
6.4k
You can use seqtk to find gaps in a fasta https://github.com/lh3/seqtk seqtk gap Usage: seqtk gap [-l 50] <in.fa>
Comment: some error in building kraken2 database
by
GenoMax
141k
> Obviously, running kraken2 after the build is complete does not produce the correct results What do you get instead? Error/no output? Ha…
Comment: Failed kmer content
by
GenoMax
141k
Can you post a screenshot of what you are referring to? Why did you choose to "clean" your data? FastQC analysis needs to be done keeping…
Comment: Help for coding: Trinity for differential gene expression studies
by
rhossen
• 0
It should be great if I have any assistance in my build up command using trinity package...
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
WouterDeCoster
47k
I want reads in a specific short interval, but if I do that with samtools view I also get reads that are spliced over that interval.
Answer: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provi…
Answer: WGCNA preservation analysis
by
Michael
54k
This seems like a model case for why we need better sustainable bioinformatics data and services. I don't know the exact background behind …
Comment: some error in building kraken2 database
by
Art1ess
• 0
this is names.dmp:![names.dmp][1] and nodes.dmp![nodes.dmp][2] [1]: /media/images/33cc9a8b-4818-48b4-913d-1c2b2185 [2]: /media/i…
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