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611 results • Page
2 of 13
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Votes
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3
votes
6
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379
views
Embryo transcriptome
database
transcriptome
SRA
updated 2 days ago by
Basti
★ 1.6k • written 4 days ago by
firefox91
• 0
6
votes
6
replies
592
views
On "wings" in volcano plots...
DEG
volcano
DGE
statistics
DE
updated 21 days ago by
ATpoint
73k • written 22 days ago by
kalavattam
▴ 120
0
votes
6
replies
383
views
variant allelic fraction
vep
updated 3 days ago by
Ram
39k • written 5 days ago by
Jom
• 0
0
votes
6
replies
1.9k
views
Variable read length distribution after cutadapt running for my ATAC-seq datasets
cutadapt
read-length
alignment
ATAC-seq
updated 2 days ago by
Ram
39k • written 3.1 years ago by
yaoyao20152031
• 0
2
votes
6
replies
389
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ
annotation
GO-term
19 days ago by
Pegasus
▴ 90
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 8 days ago by
minakshiboruahassam
• 0 • written 10 months ago by
Plus
▴ 20
4
votes
6
replies
554
views
How to pass from DNA to AA fasta
genetics
updated 18 days ago by
Buffo
★ 2.2k • written 21 days ago by
Anderson Stiward
• 0
6
votes
6
replies
2.7k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 23 days ago by
Ram
39k • written 5.5 years ago by
solveforj
▴ 20
0
votes
6
replies
1.0k
views
How do I tell piRNA population suppress TEs in a bed file?
mapping
piRNAs
TEs
updated 16 days ago by
Ram
39k • written 4.8 years ago by
jaqx008
▴ 110
3
votes
6
replies
1.8k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 23 days ago by
Ram
39k • written 5.6 years ago by
Xylanaser
▴ 80
0
votes
6
replies
622
views
Getting Error when trying to run hisat2 script! Please help!
hisat2
updated 28 days ago by
Ram
39k • written 11 months ago by
smithkthedale
▴ 10
2
votes
6
replies
607
views
how to make a venn plot with data frame in R
plot
R
Venn
19 days ago by
satva72
• 0
0
votes
6
replies
662
views
Comparative transcriptomics
rna-seq
comparative
transcriptomics
updated 22 days ago by
Vincent Laufer
★ 3.0k • written 12 months ago by
edus_bioinfo
▴ 20
2
votes
6
replies
1.0k
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 10 days ago by
Ram
39k • written 18 months ago by
kra277
• 0
0
votes
5
replies
952
views
Bioinformatics conference with possible publication
conference
updated 15 days ago by
Ram
39k • written 4.7 years ago by
bharata1803
▴ 550
3
votes
5
replies
377
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
16 days ago by
jdrohan
• 0
0
votes
5
replies
599
views
Making disjoint chromosomal sites contiguous with awk
awk
assembly
bash
sequence
updated 21 days ago by
Ram
39k • written 2.6 years ago by
selplat21
▴ 20
1
vote
5
replies
546
views
kraken on nt library
kraken
nt
18 days ago by
Francois Piumi
▴ 30
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 10 days ago by
Ram
39k • written 6.8 years ago by
Biogeek
▴ 470
2
votes
5
replies
424
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
10 days ago by
DanielEB_fisk
▴ 10
0
votes
5
replies
224
views
VCF file CSQ flag
vcf
exome-sequencing
updated 2 days ago by
Ram
39k • written 2 days ago by
Payal
▴ 140
0
votes
5
replies
960
views
bigwigs to reads in peaks
R
atac-seq
updated 2 days ago by
Ram
39k • written 2.4 years ago by
pt.taklifi
▴ 60
0
votes
5
replies
3.1k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 24 days ago by
Ram
39k • written 4.2 years ago by
marina.gerges
• 0
3
votes
5
replies
433
views
STAR error with a loop
STAR
RNA
transcriptomics
updated 29 days ago by
Ram
39k • written 6 months ago by
luzglongoria
▴ 40
0
votes
5
replies
406
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 7 days ago by
Joe
21k • written 7 days ago by
gunala.nikhil
• 0
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 22 days ago by
Ram
39k • written 5.4 years ago by
wizofe
• 0
0
votes
5
replies
2.0k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 18 days ago by
Ram
39k • written 6.9 years ago by
yoyofangliu
• 0
0
votes
5
replies
1.5k
views
terminal can't activate base automatically (conda)
conda
updated 29 days ago by
Ram
39k • written 22 months ago by
Binghong
▴ 20
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools
WES
NGS
GATK
updated 21 days ago by
Ram
39k • written 5.3 years ago by
erarroji
• 0
0
votes
5
replies
853
views
trimmomatic unknown trimmer
Trimmomatic
updated 25 days ago by
Ram
39k • written 20 months ago by
Xiaoyun
▴ 10
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 10 days ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
4
votes
5
replies
346
views
Does adding reads cause batch effects?
kallisto
RNAseq
1 day ago by
bioinfo
▴ 80
0
votes
5
replies
516
views
get allele frequency (MAF) value from snp
biomaRt
MAF
ensembl
SNP
R
27 days ago by
Barista
• 0
0
votes
5
replies
420
views
combine/merge closet variants into one from mutect2
variants
mutect2
merge
gatk
updated 25 days ago by
Istvan Albert
98k • written 4 weeks ago by
J.F.Jiang
▴ 900
0
votes
5
replies
717
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 10 days ago by
mingxi
• 0 • written 5 months ago by
elizabeth
• 0
0
votes
5
replies
807
views
Read DNA sequence from FASTA rising a subclass?
FASTA
python
updated 21 days ago by
Ram
39k • written 2.6 years ago by
Gonçalo
• 0
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 25 days ago by
Ram
39k • written 6.0 years ago by
CY
▴ 720
0
votes
5
replies
1.4k
views
Best Blast Hits from Tabular Outputs in Multiple files
python
shell
blast
updated 23 days ago by
Ram
39k • written 5.7 years ago by
trini1god
• 0
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 16 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
2
votes
4
replies
824
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 4 days ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
0
votes
4
replies
1.6k
views
RNAseq analysis: t-test ?
RNA-seq
updated 16 hours ago by
Ram
39k • written 3.1 years ago by
Novice
• 0
2
votes
4
replies
611
views
DESeq2 batch effects with nonuniform design matrix
DESeqDataSet
DESeq2
batch
updated 28 days ago by
Ram
39k • written 12 months ago by
mcsimenc
▴ 20
4
votes
4
replies
368
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 10 days ago by
Joe
21k • written 14 days ago by
antoine.fauchois92
▴ 20
1
vote
4
replies
967
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 18 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
12
votes
4
replies
505
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
25 days ago by
Rafael Soler
★ 1.2k
0
votes
4
replies
534
views
From VCF to BEAGLE format with multiple chromosomes
vcf
vcftools
beagle
gvcf
16 days ago by
Begonia_pavonina
▴ 100
0
votes
4
replies
237
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
4 days ago by
amy__
▴ 50
3
votes
4
replies
634
views
R package DESeq2 in R 3.5.1
R
updated 29 days ago by
Ram
39k • written 5 months ago by
sehriban.buyukkilic
• 0
1
vote
4
replies
2.3k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 24 days ago by
Ram
39k • written 7.1 years ago by
nchuang
▴ 260
0
votes
4
replies
389
views
What are recommended parameters for the local protein alignment ?
protein
alignment
5 days ago by
Alexander
▴ 110
611 results • Page
2 of 13
Recent Votes
Differences between trimming tools: cutadapt, bbduk and sickle
C: How sickle (adaptive trimming tool) work.
How sickle (adaptive trimming tool) work.
Comment: Help with running ATAC using Encode pipeline
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
A: Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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vkkodali_ncbi
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Recent Replies
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴ 280
Also, I would like to add that we cannot use ASCAT output for GISTIC input...since GISTIC expects all the chromosomes in the input file eve…
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴ 280
Hi, Ram thanks for the help...I figured out the issue. somehow I had duplicate files in the folder which caused the issue.
Answer: multiqc: group samples by population + boxplot ?
by
Phil Ewels
★ 1.2k
You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
Comment: Problem with GPU guppy_basecaller and SLURM
by
kenneditodd
▴ 10
Nope - but I just noticed another error message in the guppy log. I've seen some people have the same problem on nanopore community but not…
Comment: Where to get the molecular subtype information of STAD sample in TCGA
by
younglin113
▴ 50
Thanks a lot! But still a bit curious why this information is not included in GDC or UCSC xena.
Comment: CellRanger problem
by
Carlos Eduardo
• 0
I'm using cellranger mkref --genome=Viral --fasta=path.fna --genes=path.gtf I have 126G RAM
Comment: How do I run DE for TPM values (not CPM)?
by
John
• 0
Thanks, but it's giving me the error that expression object should be numeric and that there are 2 non-numeric columns (because the first t…
Comment: How do I run DE for TPM values (not CPM)?
by
LChart
2.7k
you're mixing two packages, edgeR ("dgelist") and limma ("lmFit"). Just put your log(1+TPM) matrix as the first argument to lmFit.
Answer: hisat2-align exited with value 1
by
GenoMax
130k
You only need to use the `basename` of the index when you specify it. Try hisat2 -p 4 -x /home/ngs/zebra_fish/zebra_fish -U SRR10480…
Comment: How to deal with SRA file without .SRA
by
Andy
▴ 50
Thank you Ram! Yes, I did something wrong.
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
by
Ram
39k
Exactly. Even when we were trying to leverage hail at my previous job, we ran into troubles constantly with data freezes. IMO academia is n…
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
by
Jeremy Leipzig
21k
OK hospitals in particular definitely don't want to regenerate anything as individual new samples are added to the variant store. Even the …
Comment: How to deal with SRA file without .SRA
by
Ram
39k
PRJNA is the standard NCBI BioProject prefix. There are 19 pairs of FASTQs associated with this one so you're doing something wrong
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
by
Ram
39k
> But you can't live out of your suitcase forever. I'd compare it to a local department store vs Walmart - I think cloud/distributed stora…
Comment: How do I run DE for TPM values (not CPM)?
by
John
• 0
That's what I'm trying to do but again, I'm getting an error on the last line and I'm asking how to fix it.
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