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28 results • Page
1 of 1
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2
votes
5
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203
views
kallisto index build difference according to version
index
version
kallisto
updated 17 hours ago by
dsull
★ 5.1k • written 20 hours ago by
estilo
• 0
0
votes
5
replies
271
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
updated 11 hours ago by
manaswwm
▴ 490 • written 4 days ago by
J
• 0
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 23 hours ago by
GenoMax
136k • written 19 months ago by
antoinefelden
▴ 60
0
votes
3
replies
297
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
updated 12 hours ago by
Ram
41k • written 18 days ago by
junli1988
• 0
1
vote
3
replies
304
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 19 hours ago by
GenoMax
136k • written 1 day ago by
bkffadia
• 0
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 11 hours ago by
Ram
41k • written 2.1 years ago by
Amina
• 0
0
votes
2
replies
191
views
RNA seq
Differential-gene-expression
updated 12 hours ago by
Ram
41k • written 1 day ago by
Byonkesh
• 0
0
votes
2
replies
498
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 20 hours ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
0
votes
2
replies
130
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
updated 16 hours ago by
rpolicastro
12k • written 17 hours ago by
cucindarko51
• 0
0
votes
2
replies
233
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy
CHG
CHH
CG
MeDIP
15 hours ago by
Tm
★ 1.1k
0
votes
2
replies
129
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
11 hours ago by
hemr3
• 0
0
votes
2
replies
416
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
3 hours ago by
peanut
• 0
0
votes
1
reply
104
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 5 hours ago by
dsull
★ 5.1k • written 11 hours ago by
wangjb702
• 0
0
votes
1
reply
76
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 4 hours ago by
Brian Bushnell
20k • written 7 hours ago by
isMM
• 0
0
votes
1
reply
74
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
16 hours ago by
Umer
▴ 50
0
votes
1
reply
124
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
updated 14 hours ago by
Papyrus
★ 2.7k • written 19 hours ago by
hkarakurt
▴ 180
0
votes
1
reply
97
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
6 hours ago by
enriquesan
• 0
0
votes
0
replies
43
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
8 hours ago by
S
• 0
0
votes
0
replies
55
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 8 hours ago by
Ram
41k • written 8 hours ago by
boone5jones
• 0
0
votes
0
replies
42
views
error when installing gistic2 using conda
env
gistic2
conda
7 hours ago by
luckyday1661
• 0
0
votes
0
replies
21
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
2 hours ago by
Clayton
• 0
0
votes
0
replies
190
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
promoter
motif
updated 12 hours ago by
Ram
41k • written 3 days ago by
shome
▴ 10
0
votes
0
replies
194
views
Trouble Adding Log Fold Changes to KEGG Pathway Visualization
KEGG
RStudio
updated 12 hours ago by
Ram
41k • written 24 days ago by
ramirj49
• 0
0
votes
0
replies
66
views
Microbial gene coverage from blast result
gene
coverage
13 hours ago by
aanchal.yadav
• 0
0
votes
0
replies
53
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
12 hours ago by
cyril-cros
▴ 940
0
votes
0
replies
59
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
14 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
54
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 11 hours ago by
Ram
41k • written 11 hours ago by
aswin
• 0
0
votes
0
replies
34
views
Enzyme commission number in ncbi Gene database
number
commission
enzyme
2 hours ago by
Maatary
• 0
28 results • Page
1 of 1
Recent Votes
Answer: Are we tricking ourselves with batch effect correction?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
Comment: ChatGPT optimized for bioinformatics questions
Answer: Help with gatk CreateSequenceDictionary
Answer: Help with error scanpy
Answer: FastQC without yellow box
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Recent Replies
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary
by
Chris
▴ 230
It worked! Thanks Matt!
Comment: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary
by
MatthewP
★ 1.3k
maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code
by
Brian Bushnell
20k
Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
dsull
★ 5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
Comment: Annotation GTF/GFF Arabidopsis thaliana
by
enriquesan
• 0
...........
Comment: FastQC without yellow box
by
lobelino
• 0
Thank you for your answer.
Comment: FastQC without yellow box
by
lobelino
• 0
My question is Can I trust the statistics of my data I didn't get any yellow boxes, but I got high media values. Why I didn't get any yello…
Answer: FastQC without yellow box
by
ATpoint
78k
The box is the quartiles, the red line the median. Please google how to read a box plot. Your data is good in terms of base quality.
Comment: FastQC without yellow box
by
Ram
41k
What's your question?<a href="" title="Text added because biostars parser needs it"></a>
Comment: vcftools
by
Ram
41k
Deprecated tools don't just stop producing output/errors, that's now how deprecation works.
Comment: vcftools
by
Ram
41k
> couldn't get any output What does that mean? What did you see on the screen when you ran this command? Did the command run successfully …
Comment: ChatGPT optimized for bioinformatics questions
by
Ram
41k
Wait, tinybio seems more self-aware than I thought: > **You**: Why did you give me results pertaining to sarek when I never mentioned that…
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