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567 results • Page
3 of 12
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
1.1k
views
Open source projects for canine genomics?
canine-genomics
genomics
updated 21 days ago by
Ram
39k • written 5.8 years ago by
mdbiofx
• 0
0
votes
0
replies
1.1k
views
Adding annotation tracks for multiple alignment
visualization
MAF
multiple-alignment
annotation
updated 21 days ago by
Ram
39k • written 4.7 years ago by
tim.ivanov.92
▴ 40
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly
alignment
updated 4 days ago by
Ram
39k • written 3.8 years ago by
Palgrave
▴ 110
0
votes
2
replies
1.1k
views
What programatic skills necessary for biotechnologist
biotechnology
perl
python
r
updated 25 days ago by
Ram
39k • written 6.4 years ago by
baskar.aimstar2006
• 0
0
votes
0
replies
1.1k
views
multiple Alignment Form
CIGAR
multiple-alignment
alignment
updated 21 days ago by
Ram
39k • written 6.6 years ago by
midox
▴ 290
0
votes
1
reply
1.1k
views
Mauve export similarity
multiple-sequence-alignment
mauve
updated 21 days ago by
Ram
39k • written 4.9 years ago by
firestar
★ 1.5k
0
votes
0
replies
1.1k
views
Rearragement Scaffolds for Mutiple Sequence Alignment
multiple-sequence-alignment
Post-assembly
updated 21 days ago by
Ram
39k • written 5.8 years ago by
febrigunawan48
• 0
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 21 days ago by
Ram
39k • written 2.7 years ago by
Bioinfonext
▴ 430
0
votes
0
replies
1.1k
views
Assembly error on Ipyrad step 3: ERROR IPyradError(None)
rad-seq
ipyrad
updated 1 day ago by
Ram
39k • written 3.6 years ago by
mgpastos
▴ 10
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 22 days ago by
Ram
39k • written 20 months ago by
JACKY
▴ 100
0
votes
0
replies
1.0k
views
Annotate multiple rRNAs with variable and constant regions
rRNA
multiple-alignment
SILVA
updated 21 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 13 days ago by
Ram
39k • written 4.8 years ago by
jaqx008
▴ 110
0
votes
2
replies
1.0k
views
Find most upregulated genes in one library?
EdgeR
RNA-Seq
Rsubread
updated 1 day ago by
Ram
39k • written 3.7 years ago by
williams.damon26
▴ 10
2
votes
6
replies
1.0k
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 7 days ago by
Ram
39k • written 18 months ago by
kra277
• 0
1
vote
3
replies
999
views
BLAST: overflow error
BLAST
updated 25 days ago by
Ram
39k • written 13 months ago by
antoinefelden
▴ 50
0
votes
0
replies
993
views
Python AttributeError: can't set attribute
Python
updated 25 days ago by
Ram
39k • written 16 months ago by
Muhammad
• 0
0
votes
3
replies
992
views
Explanation? Read depth, quality, and assembly accuracy in Methylome analysis context
Assembly
genome
methylation
updated 11 days ago by
Ram
39k • written 4.3 years ago by
davidfarr01
▴ 10
0
votes
0
replies
990
views
FRMA processing on two different datasets of affy u133A not same dimensions
u133A
R
frma
affy
updated 11 days ago by
Ram
39k • written 4.3 years ago by
jmannhei
▴ 10
1
vote
1
reply
990
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 13 days ago by
Ram
39k • written 4.9 years ago by
genetic
▴ 40
6
votes
9
replies
966
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 26 days ago by
Ram
39k • written 4 months ago by
luzglongoria
▴ 40
0
votes
0
replies
963
views
Standalone Blast result customization
taxonomic-assignments
updated 21 days ago by
Ram
39k • written 5.8 years ago by
apurvapunvar
• 0
1
vote
4
replies
962
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 15 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
0
votes
5
replies
951
views
Bioinformatics conference with possible publication
conference
updated 12 days ago by
Ram
39k • written 4.7 years ago by
bharata1803
▴ 550
0
votes
3
replies
940
views
Sorting by Prefix Reversal (or Flipping Pancakes) approximation
algorithms
updated 12 days ago by
Ram
39k • written 4.6 years ago by
Gustavo Temple
• 0
1
vote
0
replies
940
views
can the differences in the protein sequence be ranked according to their relevance to a certain stimuli, using a statistical method when the protein …
sequence
proteins
updated 22 days ago by
Ram
39k • written 5.9 years ago by
lochanamp
▴ 70
0
votes
2
replies
934
views
what do you mean by segment pairs
rna
protein
updated 11 days ago by
Ram
39k • written 4.4 years ago by
a4appy23
▴ 50
0
votes
0
replies
933
views
Where can I find, which yeast genes definitely have similar functions?
gene
functional-genomics
RNA-Seq
time-series
updated 7 days ago by
Ram
39k • written 6.2 years ago by
Thomas.F.Hahn3
▴ 30
0
votes
1
reply
932
views
Questions about assembly of large metagenomics dataset
assembly
metagenomics
megahit
updated 12 days ago by
Ram
39k • written 4.5 years ago by
zorrilla
• 0
1
vote
1
reply
928
views
microarray data handling
R
microarray
updated 19 days ago by
Ram
39k • written 5.5 years ago by
vincent.bioscience
• 0
0
votes
1
reply
915
views
Error: long vectors not supported yet in Monocle 2
Monocle
Monocle2
updated 25 days ago by
Ram
39k • written 18 months ago by
jason.ossart
• 0
1
vote
7
replies
905
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto
STAR
RNA-seq
Transcript_variants
20 days ago by
sohail.mbio
• 0
5
votes
7
replies
899
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 25 days ago by
Ram
39k • written 12 months ago by
rheab1230
▴ 140
7
votes
12
replies
883
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 13 days ago by
Sasha
▴ 200 • written 19 days ago by
Chris
▴ 100
0
votes
0
replies
883
views
Using phosphonormalizer in phosphoproteomics experiments
phosphonormalizer
phosphoproteomics
Normalization
updated 22 days ago by
Ram
39k • written 5.9 years ago by
sohrabsaraei101101
• 0
0
votes
1
reply
873
views
Masters in Bioinformatics
masters
structural-bioinformatics
assistantship
updated 5 days ago by
Ram
39k • written 3.9 years ago by
Manvitha Reddy
▴ 10
0
votes
0
replies
866
views
Error processing Hi-data using HiCUP
NGS
HiCUP
Hi-C
updated 6 days ago by
Ram
39k • written 4.0 years ago by
srhic
▴ 40
2
votes
3
replies
863
views
Freebayes command stopped due to lack of space
freebayes
SNP-calling
updated 13 days ago by
Ram
39k • written 5.0 years ago by
amcheroo
• 0
1
vote
8
replies
862
views
Betacoronavirus.00.nsq error
corona
biostars
updated 22 days ago by
Ram
39k • written 16 months ago by
Sam
• 0
0
votes
4
replies
861
views
bowtie2 -all ... multiple alignment Chip-seq
bowtie2
alignment
ChIP-Seq
multiple-alignment
updated 21 days ago by
Ram
39k • written 3.6 years ago by
poltora4enko
▴ 10
0
votes
5
replies
852
views
trimmomatic unknown trimmer
Trimmomatic
updated 22 days ago by
Ram
39k • written 20 months ago by
Xiaoyun
▴ 10
0
votes
1
reply
849
views
Get publication counts per gene per year
eutilities
updated 7 days ago by
Ram
39k • written 4.2 years ago by
abhijit.synl
▴ 60
0
votes
0
replies
845
views
How do I get the alignment score from multiple alignment in MAFFT
T-coffee
MAFFT
multiple-alignment
updated 21 days ago by
Ram
39k • written 2.8 years ago by
mail2steff
▴ 60
1
vote
9
replies
843
views
Couldn't get a file descriptor referring to the console multiqc
multiqc
updated 25 days ago by
Ram
39k • written 11 months ago by
smithkthedale
▴ 10
0
votes
2
replies
841
views
BLAST ERROR Too many positional arguments (1)
blastp
blast
updated 25 days ago by
Ram
39k • written 13 months ago by
Paula
▴ 60
0
votes
2
replies
838
views
error while running job in michigan imputation server
vcf
reference-genome
michigan-imputation-server
updated 19 days ago by
Sasha
▴ 200 • written 17 months ago by
rheab1230
▴ 140
0
votes
0
replies
838
views
Time series analysis for RNA-seq paired samples
TimeSeriesExperiment
RNA-Seq
time-series
updated 7 days ago by
Ram
39k • written 3.3 years ago by
essief
• 0
2
votes
4
replies
823
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 1 day ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
0
votes
0
replies
820
views
How many works can clustalw can support at the same time?
clustalw
updated 14 days ago by
Ram
39k • written 5.0 years ago by
ricfoz
▴ 80
0
votes
1
reply
813
views
Filtering for homozygous reference alleles
SNP
sequence
genome
updated 4 days ago by
Ram
39k • written 3.7 years ago by
AGE
▴ 30
0
votes
2
replies
812
views
How to get a list of aligned read and reference positions using samtools
samtools
api
htslib
Cpp
c
updated 15 days ago by
Ram
39k • written 3.1 years ago by
Aref.Ariyapour
• 0
567 results • Page
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Recent Votes
ChatGPT optimized for bioinformatics questions
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Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
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Comment: switching from illumination to NEB prep kits
by
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129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
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yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values
by
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72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
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https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values
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The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
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Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
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Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
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Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
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Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
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4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
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by
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★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
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Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
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melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
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