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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 14 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 5 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 14 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
RNA-seq power estimation using ssizeRNA program
Answer: WGCNA preservation analysis
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
ISCN annotation for SV/CN VCF files
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
Trimming sequences based on NCBI contamination screen report
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★ 2.4k
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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11"
by
Dylan
• 0
> (which is weird, if it's in proper pair, read and its mate should be both mapped) So that was my thought as well, I think the code you l…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Ram
43k
> several single cell samples At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
Answer: Difference between samtools "-f 9" and "-f 11"
by
Pierre Lindenbaum
161k
9: read must be paired AND mate must be unmapped 11: read must be paired AND mapped in proper pair AND mate must be unmapped (which is w…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser
by
atowns21
• 0
could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
This is how my .fam file looks like ![enter image description here][1] [1]: /media/images/caccd97c-3606-48d2-aa32-423a9882 And I run …
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
> linked to a list of grants Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
Answer: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Hi Dominick, One thing I am not sure of is, how is it that you got the other PMID in the first place? The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
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