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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment
FastTree
Phylogenetic Tree
5.3 years ago by
Moses
▴ 150
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.7 years ago by
lieven.sterck
15k • written 3.7 years ago by
schlogl
▴ 160
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.7 years ago by
Mostafa
▴ 20
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.3 years ago by
Chaimaa
▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 2.3 years ago by
Ram
43k • written 9.8 years ago by
BDK_compbio
▴ 140
3
votes
16
replies
1.6k
views
Problem, getting information only from the last row and not from all the rows
perl
6.0 years ago by
ArusjakGevorgyan
▴ 30
0
votes
16
replies
3.8k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 11 months ago by
Ram
43k • written 5.9 years ago by
rororo
▴ 10
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
9
votes
16
replies
3.8k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 13 months ago by
Ram
43k • written 5.7 years ago by
marongiu.luigi
▴ 710
0
votes
16
replies
2.8k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 13 months ago by
Ram
43k • written 20 months ago by
yoser4
▴ 10
7
votes
16
replies
3.9k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing
genome-sequence
fastqc
genome
sequence
4.1 years ago by
Researcher
▴ 20
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 9 weeks ago by
Ram
43k • written 10 weeks ago by
Eric
• 0
13
votes
16
replies
6.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
7.3 years ago by
Paul
★ 1.5k
4
votes
16
replies
1.8k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
updated 10 weeks ago by
Ram
43k • written 7 months ago by
ella
• 0
13
votes
16
replies
7.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
5.3 years ago by
DNAngel
▴ 250
1
vote
16
replies
2.0k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq
hisat2
samtools
mapping
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
Vasu
▴ 770
1
vote
16
replies
2.7k
views
Merging fastq files from two experiments
FASTQ
NGS
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
zizigolu
★ 4.3k
4
votes
16
replies
4.5k
views
Working with human database in Kraken
RNA-Seq
next-gen
genome
7.9 years ago by
Ron
★ 1.2k
3
votes
16
replies
4.1k
views
GC content of 10x Genomics
fastqc
10x
GC content
updated 3.7 years ago by
Eugene A
▴ 180 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
16
replies
7.0k
views
After sorting bam file not able to index ?
alignment
next-gen
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
sunnykevin97
▴ 980
5
votes
16
replies
6.2k
views
Remove duplicate lines based on specific columns
r
python
intersect
reads
updated 5.6 years ago by
Ram
43k • written 5.6 years ago by
dzisis1986
▴ 70
16
votes
16
replies
3.2k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
6.1 years ago by
bioinfo456
▴ 150
4
votes
16
replies
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.7 years ago by
Biostar
20 • written 7.5 years ago by
lu.ne
▴ 70
2
votes
16
replies
1.9k
views
I want to know is it a true method ?
vcf
SNP
realignment
6.1 years ago by
Siavash Salek Ardestani
▴ 20
5
votes
16
replies
4.3k
views
plotting problem with loop in R
R
plot
4.9 years ago by
smyiz
▴ 30
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools
sort
11.0 years ago by
chentong.biology
▴ 50
1
vote
15
replies
3.7k
views
Can I use PICARD (SortSam) instead of SAMTOOLS (sort) for sorting bam files in RNAseq pipeline where HISAT2 is used for alignment.
RNA-Seq
software error
sequencing
next-gen
6.0 years ago by
shuksi1984
▴ 60
0
votes
15
replies
2.0k
views
compare two NCBI ftp tables
table
NCBI
updated 2.9 years ago by
Ram
43k • written 2.9 years ago by
Debut
▴ 20
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq
differential expression
4.5 years ago by
guillaume.rbt
★ 1.0k
1
vote
15
replies
3.7k
views
Fastx quality filter
next-gen
RNA-Seq
software error
sequencing
updated 7.4 years ago by
Ram
43k • written 7.4 years ago by
kriti.awasthi23
▴ 10
5
votes
15
replies
1.5k
views
Get list of gene signatures published
bailey
genes
subtype
pancreas
3.3 years ago by
sabin
▴ 50
0
votes
15
replies
2.4k
views
pathway analysis tools for xenopus
pathways
omics
xenopus
updated 7.8 years ago by
EagleEye
7.5k • written 7.8 years ago by
mike
▴ 90
0
votes
15
replies
3.2k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 2.5 years ago by
greekkey
▴ 20 • written 2.8 years ago by
smrutimayipanda
▴ 20
6
votes
15
replies
2.5k
views
processing in strelka2 with multiples bam file in directory
strelka2
updated 2.3 years ago by
aldhairmedico
▴ 70 • written 4.4 years ago by
bioguy24
▴ 230
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast
alignment
rna-seq
gene
updated 16 months ago by
Ram
43k • written 8.9 years ago by
gchaves
• 0
1
vote
15
replies
1.5k
views
How to reduce my dataset in order to plot it?
correlation
igraph
updated 4.7 years ago by
Biostar
20 • written 4.9 years ago by
pablo
▴ 300
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by
benjyrolls
▴ 70
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping
coverage
DNA
genomic
updated 2.7 years ago by
ATpoint
82k • written 2.7 years ago by
Lila M
★ 1.2k
1
vote
15
replies
3.3k
views
How to perform multiple alignment using MAFFT?
genome
alignment
gene
sequence
3.1 years ago by
anikcropscience
▴ 230
3
votes
15
replies
2.0k
views
Overlapping regions in a BED file
regions
BED
Sequence
exons
annotation
22 months ago by
Matej
• 0
3
votes
15
replies
5.6k
views
Pairwise sequence alignment with Biojava?
sequence-alignment
biojava
java
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Bioaln
▴ 360
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
10 months ago by
Chris
▴ 260
2
votes
15
replies
2.2k
views
to get each covariate with PC loading in PCA
RNA-seq
PCA
5.3 years ago by
Grace_G
▴ 20
3
votes
15
replies
2.8k
views
fastq reads with primers and truseq indexed adapter
sequencing
next-gen
sequence
7.1 years ago by
jomo018
▴ 720
2
votes
15
replies
4.6k
views
Error when indexing a bcf file
vcf
bcf
5.7 years ago by
Famf
▴ 30
2
votes
15
replies
1.6k
views
How to call all the allele in samples
SNP
6.0 years ago by
Kritika
▴ 260
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.4 years ago by
Farbod
★ 3.4k
0
votes
15
replies
3.3k
views
bcftools multiple samples
snp
4.5 years ago by
evelyn
▴ 230
1,000 results • Page
4 of 20
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
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Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
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Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
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by
Expert
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Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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by
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82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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Ruqaiya
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This the tool still problematic?
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Ruqaiya
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Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
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Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
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Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
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I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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