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510 results • Page
2 of 11
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
1.5k
views
how to detect the presence of Integrative and conjugative elements in bacterial genome.
Genomics
updated 14 days ago by
Ram
39k • written 5.7 years ago by
Optimist
▴ 180
0
votes
1
reply
1.5k
views
Why does shoremap calculate allele frequency this way?
shoremap
allele-frequency
updated 13 days ago by
Ram
39k • written 5.7 years ago by
emilywynn6
▴ 10
2
votes
7
replies
1.5k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 8 days ago by
Ram
39k • written 5.2 years ago by
navela78
▴ 70
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 5 hours ago by
Ram
39k • written 6.8 years ago by
statfa
▴ 720
0
votes
0
replies
1.5k
views
CD-hit records matching and parsing
bash
python
cd-hit
text-processing
updated 4 days ago by
Ram
39k • written 4.2 years ago by
mnmalash
• 0
0
votes
5
replies
1.4k
views
Best Blast Hits from Tabular Outputs in Multiple files
python
shell
blast
updated 13 days ago by
Ram
39k • written 5.6 years ago by
trini1god
• 0
1
vote
2
replies
1.4k
views
Getting full list for DEGs in Noiseq
RNA-Seq
updated 12 days ago by
Ram
39k • written 5.4 years ago by
mubangafchama
▴ 10
0
votes
0
replies
1.4k
views
envelope and alignment coordinates in hmmsearch result
hmmer
sequence
alignment
hmmsearch
updated 4 days ago by
Ram
39k • written 4.4 years ago by
sanjeet00001992
• 0
0
votes
5
replies
1.4k
views
terminal can't activate base automatically (conda)
conda
updated 19 days ago by
Ram
39k • written 21 months ago by
Binghong
▴ 20
2
votes
4
replies
1.4k
views
Gettin Consensus From Multiple Whole Genomes
multiple-sequence-alignment
whole-genome-alignment
updated 14 days ago by
Ram
39k • written 6.4 years ago by
nilaylale88
• 0
1
vote
3
replies
1.4k
views
How to check quality of multiple sequence alignment (MSA)?
MSA
multiple-sequence-alignment
R
updated 14 days ago by
Ram
39k • written 3.2 years ago by
Chirag Parsania
★ 2.0k
0
votes
3
replies
1.4k
views
SNPEff not showing SNP
snpEff
variant-annotation
SNP
updated 7 days ago by
Ram
39k • written 5.1 years ago by
sanjay.bpkihs
• 0
1
vote
3
replies
1.4k
views
Alignment of two different file format
alignment
updated 14 days ago by
Ram
39k • written 5.8 years ago by
amoolya36
• 0
6
votes
7
replies
1.4k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters
Algorithm
Software
updated 18 days ago by
Ram
39k • written 6.0 years ago by
nilo
▴ 90
0
votes
0
replies
1.4k
views
How to use SABmark 1.65 as a benchmark?
multiple-sequence-alignment
SABmark
updated 14 days ago by
Ram
39k • written 6.7 years ago by
Jay
• 0
0
votes
1
reply
1.4k
views
Pipeline for scRNA-Seq
next-gen
R
RNA-Seq
updated 13 days ago by
Ram
39k • written 5.6 years ago by
alpha09
▴ 10
0
votes
1
reply
1.4k
views
Extract sequence subset from multiple sequence alignment based on position in a specific species.
R
Biostrings
msa
updated 19 days ago by
rohitsatyam102
▴ 690 • written 2.6 years ago by
nad7wf
• 0
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 5 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
1
vote
1
reply
1.3k
views
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
Bash
Shell
HISAT2
updated 4 days ago by
Ram
39k • written 4.3 years ago by
RNAseqer
▴ 240
0
votes
4
replies
1.3k
views
File not found error on program installation.
samtools
htslib
Cpp
updated 8 days ago by
Ram
39k • written 3.6 years ago by
M.O.L.S
▴ 100
0
votes
3
replies
1.3k
views
Cannot open BAM files with the SeqAn library
cpp
seqan
Bam
sequencing
updated 8 days ago by
Ram
39k • written 5.2 years ago by
omariqbal2017
• 0
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools
WES
NGS
GATK
updated 11 days ago by
Ram
39k • written 5.3 years ago by
erarroji
• 0
0
votes
0
replies
1.3k
views
Human Breast Cancer Panel QIAseq manifest
manifest
panel
updated 15 days ago by
Ram
39k • written 5.9 years ago by
fabbri.marco
▴ 10
3
votes
8
replies
1.3k
views
Kallisto mapping paired end
Kallisto
mapping
updated 17 days ago by
Ram
39k • written 15 months ago by
Dk
▴ 20
0
votes
4
replies
1.3k
views
How can I extract position information from multiple alignment format?
CLUSTAL
MAFFT
multiple-alignment
updated 14 days ago by
Ram
39k • written 3.3 years ago by
haewon
• 0
3
votes
4
replies
1.3k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics
phasing
fastPHASE
updated 8 days ago by
Ram
39k • written 5.2 years ago by
lakemonster
▴ 10
0
votes
0
replies
1.3k
views
Cuffdiff with 2 conditions and time series
cuffdiff
time-series
RNA-Seq
transcriptome
updated 5 hours ago by
Ram
39k • written 6.2 years ago by
KL
• 0
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment
hisat2
updated 15 days ago by
Ram
39k • written 19 months ago by
Xiaoyun
▴ 10
1
vote
0
replies
1.2k
views
Align two single cell experiments
R
single-cell
updated 4 days ago by
Ram
39k • written 4.5 years ago by
elb
▴ 230
0
votes
0
replies
1.2k
views
Counting the number of paralogues for mouse genes gives me the wrong frequency
ensembl
R
biomart
updated 11 days ago by
Ram
39k • written 5.3 years ago by
up728920
• 0
0
votes
3
replies
1.2k
views
Ensemble file Mus_musculus.GRCm38.dna.primary_assembly.fa.gz unzipping to incorrect contents
genome
RSEM
Ensembl
updated 15 days ago by
Ram
39k • written 19 months ago by
jennifer.conrad84
▴ 10
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 15 days ago by
Ram
39k • written 5.9 years ago by
CY
▴ 710
1
vote
0
replies
1.2k
views
sequence alignment using edlib c++ library
cpp
alignment
updated 8 days ago by
Ram
39k • written 4.8 years ago by
BDK_compbio
▴ 130
0
votes
0
replies
1.1k
views
EDGE microarray time series analysis fit_models() ERROR
microarray
time-series
updated 5 hours ago by
Ram
39k • written 5.4 years ago by
tleona3
▴ 10
0
votes
4
replies
1.1k
views
No space separating sequence and name PopArt error !?
popart
traits
haplotypes
python
updated 18 days ago by
Ram
39k • written 2.0 years ago by
matache.razvan911
• 0
0
votes
0
replies
1.1k
views
Open source projects for canine genomics?
canine-genomics
genomics
updated 14 days ago by
Ram
39k • written 5.7 years ago by
mdbiofx
• 0
0
votes
0
replies
1.1k
views
Adding annotation tracks for multiple alignment
visualization
MAF
multiple-alignment
annotation
updated 14 days ago by
Ram
39k • written 4.7 years ago by
tim.ivanov.92
▴ 40
0
votes
2
replies
1.1k
views
What programatic skills necessary for biotechnologist
biotechnology
perl
python
r
updated 18 days ago by
Ram
39k • written 6.3 years ago by
baskar.aimstar2006
• 0
0
votes
0
replies
1.1k
views
multiple Alignment Form
CIGAR
multiple-alignment
alignment
updated 14 days ago by
Ram
39k • written 6.6 years ago by
midox
▴ 290
0
votes
0
replies
1.1k
views
Rearragement Scaffolds for Mutiple Sequence Alignment
multiple-sequence-alignment
Post-assembly
updated 14 days ago by
Ram
39k • written 5.8 years ago by
febrigunawan48
• 0
0
votes
1
reply
1.1k
views
Mauve export similarity
multiple-sequence-alignment
mauve
updated 14 days ago by
Ram
39k • written 4.8 years ago by
firestar
★ 1.5k
3
votes
6
replies
1.1k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq
PYTHON
R
bash
updated 14 days ago by
Ram
39k • written 2.7 years ago by
Bioinfonext
▴ 430
0
votes
2
replies
1.0k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
URL
R
updated 15 days ago by
Ram
39k • written 19 months ago by
JACKY
▴ 80
0
votes
0
replies
1.0k
views
Annotate multiple rRNAs with variable and constant regions
rRNA
multiple-alignment
SILVA
updated 14 days ago by
Ram
39k • written 5.9 years ago by
predeus
★ 1.9k
0
votes
6
replies
1.0k
views
How do I tell piRNA population suppress TEs in a bed file?
mapping
piRNAs
TEs
updated 6 days ago by
Ram
39k • written 4.8 years ago by
jaqx008
▴ 110
2
votes
6
replies
999
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 6 hours ago by
Ram
39k • written 18 months ago by
kra277
• 0
0
votes
3
replies
989
views
Explanation? Read depth, quality, and assembly accuracy in Methylome analysis context
Assembly
genome
methylation
updated 4 days ago by
Ram
39k • written 4.3 years ago by
davidfarr01
▴ 10
0
votes
0
replies
989
views
FRMA processing on two different datasets of affy u133A not same dimensions
u133A
R
frma
affy
updated 3 days ago by
Ram
39k • written 4.2 years ago by
jmannhei
▴ 10
1
vote
3
replies
986
views
BLAST: overflow error
BLAST
updated 18 days ago by
Ram
39k • written 13 months ago by
antoinefelden
▴ 50
1
vote
1
reply
985
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 6 days ago by
Ram
39k • written 4.9 years ago by
genetic
▴ 40
510 results • Page
2 of 11
Recent Votes
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
Answer: Salmon Index
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Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
• 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Comment: Salmon Index
by
ashleymb1116
• 0
Thank you, yes I am using the newer version of Ensembl. Above with Arabidopsis is the example Salmon gave, I am using the Bos Taurus files.…
Comment: Query qbout single cell sequencing
by
Ram
39k
Show us your exact cellranger and STARsolo commands, the full output to STARsolo as well as your thoughts on why it's not working for you.
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