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117,088 results • Page
1 of 2342
Sort: Rank
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Votes
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0
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0
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6
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq
seurat
miloR
10 minutes ago by
shuaizh117
▴ 10
1
vote
1
reply
57
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 2 hours ago by
Jeremy
▴ 910 • written 3 hours ago by
Mohamed Samir
▴ 30
0
votes
0
replies
33
views
Phyloseq returning black bars for plot_bar
phyloseq
bioconductor
R
4 hours ago by
Jacob
• 0
1
vote
8
replies
803
views
Random Access remote BAM files
htslib
BAM
updated 5 hours ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 10
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
3
replies
117
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
48
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
6 hours ago by
dglad
• 0
0
votes
4
replies
147
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
6 hours ago by
reza
▴ 300
0
votes
1
reply
69
views
Flag multiple filtering steps on VCF files using VEP
FILTERING
VEP
VCF
updated 6 hours ago by
Pierre Lindenbaum
162k • written 7 hours ago by
avelarbio46
▴ 30
0
votes
1
reply
89
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
Fossil
• 0
1
vote
1
reply
128
views
Construction of circos plot from WGS data
WGS
Circos
updated 8 hours ago by
Ram
44k • written 15 hours ago by
Anitha
▴ 10
1
vote
3
replies
182
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 10 hours ago by
GenoMax
142k • written 10 hours ago by
Wilber0x
▴ 50
0
votes
0
replies
60
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
alignment
updated 8 hours ago by
Ram
44k • written 10 hours ago by
Melissa
• 0
5
votes
3
replies
153
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 12 hours ago by
GenoMax
142k • written 12 hours ago by
Christopher
▴ 10
0
votes
0
replies
58
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
12 hours ago by
Tim
• 0
1
vote
5
replies
195
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
updated 8 hours ago by
Ram
44k • written 12 hours ago by
anikcropscience
▴ 230
0
votes
0
replies
68
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
Zea-mays
R
updated 8 hours ago by
Ram
44k • written 12 hours ago by
letizia.ottaviani
• 0
0
votes
6
replies
221
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 6 hours ago by
ATpoint
82k • written 15 hours ago by
machaalani29
• 0
0
votes
0
replies
66
views
News:
Bioinformatic Analysis of Transposable Elements course
Genome-Annotation
TE
Manual-Curation
Transposable-Elements
updated 8 hours ago by
Ram
44k • written 16 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
98
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 8 hours ago by
Ram
44k • written 16 hours ago by
ashkan
▴ 160
3
votes
1
reply
129
views
vg autoindex seems stuck after a week of running
vg
pangenome
updated 17 hours ago by
Jouni Sirén
▴ 380 • written 20 hours ago by
StevieP
▴ 10
0
votes
0
replies
81
views
MAFFT alignment report
RNA
Alignment
MAFFT
Linux
updated 8 hours ago by
Ram
44k • written 18 hours ago by
Ghada
• 0
0
votes
3
replies
264
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 19 hours ago by
colindaven
6.4k • written 2 days ago by
Bjorn
• 0
0
votes
1
reply
124
views
How to get 2 seurat objects into a DEseq
Seurat
DEseq
updated 8 hours ago by
Ram
44k • written 1 day ago by
He11oJe11o
• 0
0
votes
0
replies
68
views
Rescaling normalized enrichment score (NES)
heatmap
19 hours ago by
CTLong
▴ 110
0
votes
2
replies
140
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
21 hours ago by
kmat
• 0
0
votes
1
reply
124
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
updated 19 hours ago by
ATpoint
82k • written 22 hours ago by
rj.rezwan
• 0
0
votes
1
reply
128
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 19 hours ago by
ATpoint
82k • written 22 hours ago by
Varsha
• 0
0
votes
5
replies
156
views
samtools write-index
samtools
1 hour ago by
LucisTheFather
• 0
0
votes
0
replies
80
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
1 day ago by
dlera.lozano
▴ 10
0
votes
0
replies
95
views
DIFFBIND boxplot results, p value not significant
DiffBind
ChIP-seq
11 hours ago by
RD
▴ 10
3
votes
6
replies
305
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 8 hours ago by
Ram
44k • written 1 day ago by
anasjamshed
▴ 120
0
votes
1
reply
157
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 1 day ago by
andersdetermig
▴ 20 • written 2 days ago by
Christopher
• 0
0
votes
2
replies
256
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
1 day ago by
ezz3
• 0
1
vote
10
replies
594
views
Add stats to the plot
R
19 hours ago by
Ghada
• 0
0
votes
4
replies
207
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
1 day ago by
shpak.max
▴ 50
2
votes
4
replies
230
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
6 hours ago by
Arton
▴ 10
1
vote
3
replies
180
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 15 hours ago by
GenoMax
142k • written 1 day ago by
s
• 0
0
votes
3
replies
170
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 1 day ago by
GenoMax
142k • written 1 day ago by
bioinfo
▴ 150
1
vote
2
replies
160
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
9 hours ago by
Tuấn Anh
• 0
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 1 day ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
1
vote
3
replies
282
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
1 day ago by
Pegasus
▴ 100
0
votes
2
replies
178
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
1 day ago by
Shukai
• 0
1
vote
3
replies
184
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 1 day ago by
Pierre Lindenbaum
162k • written 1 day ago by
mrk
• 0
0
votes
3
replies
228
views
z-score of gene set
z-score
scRNA
gene-set
20 hours ago by
Hien
• 0
3
votes
2
replies
194
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 15 hours ago by
GenoMax
142k • written 1 day ago by
ashkan
▴ 160
0
votes
0
replies
94
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 1 day ago by
GenoMax
142k • written 1 day ago by
LuciaNhu
• 0
1
vote
2
replies
174
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 1 day ago by
Ram
44k • written 1 day ago by
Harshita
• 0
3
votes
0
replies
113
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 1 day ago by
Ram
44k • written 1 day ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
118
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 1 day ago by
Ram
44k • written 1 day ago by
Fabio Marroni
★ 3.0k
117,088 results • Page
1 of 2342
Recent Votes
Error when looping over multiple columns in a data frame in R
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
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Comment: samtools write-index
by
LucisTheFather
• 0
``` -o alignment.sorted.bam##idx##alignment.sorted.bam.bai ``` This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index
by
LucisTheFather
• 0
Really appreciate your help Pierre! I am a little bit confused btw. do you mean this: ``` rm -vf alignment.sorted.bam.bai minimap2 -ax map-…
Comment: samtools write-index
by
LucisTheFather
• 0
Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests) and none of…
Comment: Which 1000 genomes 30x files should I use for imputation?
by
David-walson
• 0
Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
Comment: MAUVE: No gene annotations in Genbank file alignments
by
pramach1
▴ 40
The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
Answer: Error when looping over multiple columns in a data frame in R
by
Jeremy
▴ 910
First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
bk11
★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
• 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
by
ATpoint
82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
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