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117,080 results • Page
1 of 2342
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Trimmomatic running but files containing purged reads are empty
sequence
fastqc
fastq
trimmomatic
6 minutes ago by
Wilber0x
▴ 50
0
votes
0
replies
11
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
sequence
alignment
gene
genome
25 minutes ago by
Melissa
• 0
4
votes
3
replies
62
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 56 minutes ago by
GenoMax
142k • written 1 hour ago by
Christopher
• 0
0
votes
0
replies
21
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
2 hours ago by
Tim
• 0
1
vote
4
replies
78
views
How to get the ratio of allele counts from GATK derived VCF file?
SNP
Freebayes
GATK
Bioinformatics
VCF
2 hours ago by
anikcropscience
▴ 230
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
0
replies
32
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
R
mays
Zea
analysis
2 hours ago by
letizia.ottaviani
• 0
0
votes
4
replies
141
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 2 hours ago by
GenoMax
142k • written 5 hours ago by
machaalani29
• 0
1
vote
0
replies
52
views
Construction of circos plot from WGS data
Data
Plot
WGS
Circos
Input
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
Anitha
▴ 10
0
votes
0
replies
43
views
News:
Bioinformatic Analysis of Transposable Elements course
ManualCuration
GenomeAnnotation
Transposable-Elements
TE
5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
76
views
No output when converting transcript IDs to gene symbols
RNAseq
updated 5 hours ago by
ATpoint
82k • written 6 hours ago by
ashkan
▴ 160
3
votes
1
reply
112
views
vg autoindex seems stuck after a week of running
vg
pangenome
updated 7 hours ago by
Jouni Sirén
▴ 380 • written 10 hours ago by
StevieP
▴ 10
0
votes
0
replies
57
views
MAFFT alignment report
sequence
RNA
Alignment
Linux
updated 1 hour ago by
GenoMax
142k • written 8 hours ago by
Ghada
• 0
0
votes
3
replies
248
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 8 hours ago by
colindaven
6.4k • written 1 day ago by
Bjorn
• 0
0
votes
1
reply
108
views
How to get 2 seurat objects into a DEseq
help
troubleshoot
updated 9 hours ago by
ultraanfibio
▴ 30 • written 15 hours ago by
He11oJe11o
• 0
0
votes
0
replies
51
views
Rescaling normalized enrichment score (NES)
heatmap
9 hours ago by
CTLong
▴ 110
0
votes
2
replies
117
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
11 hours ago by
kmat
• 0
0
votes
1
reply
105
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
updated 9 hours ago by
ATpoint
82k • written 12 hours ago by
rj.rezwan
• 0
0
votes
1
reply
112
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 9 hours ago by
ATpoint
82k • written 12 hours ago by
Varsha
• 0
0
votes
2
replies
105
views
samtools write-index
samtools
updated 2 hours ago by
GenoMax
142k • written 13 hours ago by
LucisTheFather
• 0
0
votes
0
replies
65
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
14 hours ago by
dlera.lozano
▴ 10
0
votes
0
replies
76
views
DIFFBIND boxplot results, p value not significant
DiffBind
ChIP-seq
1 hour ago by
RD
▴ 10
3
votes
6
replies
285
views
Problem in getting geo file through GEOQUERY
file
download
Geo
18 hours ago by
anasjamshed
▴ 120
0
votes
1
reply
145
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 19 hours ago by
andersdetermig
▴ 20 • written 1 day ago by
Christopher
• 0
0
votes
2
replies
209
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
19 hours ago by
ezz3
• 0
1
vote
10
replies
572
views
Add stats to the plot
R
9 hours ago by
Ghada
• 0
0
votes
4
replies
191
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
19 hours ago by
shpak.max
▴ 50
0
votes
2
replies
138
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated 20 hours ago by
LChart
3.9k • written 22 hours ago by
Arton
▴ 10
1
vote
3
replies
160
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 5 hours ago by
GenoMax
142k • written 21 hours ago by
s
• 0
0
votes
3
replies
154
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 21 hours ago by
GenoMax
142k • written 21 hours ago by
bioinfo
▴ 150
1
vote
1
reply
96
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
updated 22 hours ago by
GenoMax
142k • written 22 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 23 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
1
vote
3
replies
267
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
14 hours ago by
Pegasus
▴ 100
0
votes
2
replies
167
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
170
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 21 hours ago by
Pierre Lindenbaum
162k • written 1 day ago by
mrk
• 0
0
votes
3
replies
216
views
z-score of gene set
z-score
scRNA
gene-set
10 hours ago by
Hien
• 0
2
votes
2
replies
170
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 5 hours ago by
GenoMax
142k • written 1 day ago by
ashkan
▴ 160
0
votes
0
replies
84
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
162
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 23 hours ago by
Ram
44k • written 1 day ago by
Harshita
• 0
3
votes
0
replies
101
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 22 hours ago by
Ram
44k • written 1 day ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
105
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 22 hours ago by
Ram
44k • written 1 day ago by
Fabio Marroni
★ 3.0k
3
votes
5
replies
452
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
1 day ago by
beantkapoor16
▴ 10
0
votes
1
reply
123
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 1 day ago by
DBScan
▴ 300 • written 1 day ago by
brunomiwa
• 0
0
votes
0
replies
82
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
1 day ago by
Ayda Ecem
• 0
0
votes
3
replies
153
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 22 hours ago by
Ram
44k • written 1 day ago by
pirku
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 22 hours ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
551
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 1 day ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
85
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
1 day ago by
Yao
▴ 30
1
vote
1
reply
732
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
117,080 results • Page
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Classifying normal vs cancer tissues from mutational data
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Comment: FastQC interpretation - 16S sequencing
Comment: FastQC interpretation - 16S sequencing
Answer: vg autoindex seems stuck after a week of running
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Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing
by
Christopher
• 0
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
But I used the same bam files in both freebayes and GATK. Even the overlapping SNPs from both software are giving different estimates in te…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
Pierre Lindenbaum
162k
may be downsampling(?), QC failing reads ?
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
Thank you. However, I extracted the AD for each SNP that gives two numbers separated by a comma. I guess the first one is for reference and…
Answer: How to get the ratio of allele counts from GATK derived VCF file?
by
Pierre Lindenbaum
162k
> However, I am doing SNP calling using GATK, but there is no such information field for reference and alternate allele counts. it's in …
Comment: samtools write-index
by
GenoMax
142k
> The index file is older than the data file: alignment.sorted.bam.bai I don't think that warning is going to cause any issues. Not sure w…
Comment: samtools write-index
by
Pierre Lindenbaum
162k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o alignment.sorted.bam` should be enoug…
Answer: from CRAM to fastq
by
Pierre Lindenbaum
162k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq
by
machaalani29
• 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq
by
machaalani29
• 0
the option -c is to compress the file
Comment: from CRAM to fastq
by
GenoMax
142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R
by
GenoMax
142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
Activities with `cucurbitacin A`: https://www.ebi.ac.uk/chembl/web_components/explore/activities/STATE_ID:RHxG8uDfrtbmiyaY55ic-w%3D%3D `cu…
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