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29 results • Page
1 of 1
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Views
Votes
Replies
6
votes
4
replies
12k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 2 hours ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
9
votes
23
replies
9.7k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
37 minutes ago by
vytarasov
▴ 180
9
votes
7
replies
7.0k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 1 hour ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 20 hours ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
1
vote
4
replies
474
views
cellranger error message
multiplexing
cellranger
updated 22 hours ago by
Max
• 0 • written 12 weeks ago by
Alivia
▴ 10
1
vote
4
replies
387
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 18 hours ago by
GenoMax
142k • written 23 days ago by
aniigodwinn
• 0
0
votes
10
replies
307
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 14 hours ago by
swbarnes2
14k • written 21 hours ago by
Tuck898
• 0
1
vote
4
replies
284
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
16 hours ago by
rackbersingh
• 0
0
votes
2
replies
254
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 18 hours ago by
GenoMax
142k • written 7 days ago by
Ximena
• 0
3
votes
4
replies
247
views
Truncated metadata file report from ENA Portal API
ena
python
18 hours ago by
Giulia
• 0
0
votes
4
replies
240
views
Correlation Analysis
statistics
methylation
NGS
expression
5 hours ago by
Researcher
▴ 30
0
votes
5
replies
197
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
21 hours ago by
SilhouetteQ
• 0
0
votes
2
replies
171
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 16 hours ago by
Ram
43k • written 1 day ago by
sainavyav22
• 0
1
vote
3
replies
170
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 16 hours ago by
Ram
43k • written 23 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
160
views
How are score_weights calculated in this code?
single-cell
4 hours ago by
carolofharvest
▴ 40
3
votes
3
replies
143
views
what is another word for a BLAST "hit"?
blast
alignment
16 hours ago by
dec986
▴ 380
1
vote
3
replies
136
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 14 hours ago by
GenoMax
142k • written 15 hours ago by
meck
• 0
0
votes
1
reply
135
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 18 hours ago by
curious
▴ 750 • written 1 day ago by
SeoGyun
• 0
1
vote
2
replies
125
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
3 hours ago by
rackbersingh
• 0
0
votes
0
replies
110
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
updated 14 hours ago by
GenoMax
142k • written 9 days ago by
meck
• 0
0
votes
1
reply
108
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 16 hours ago by
Ram
43k • written 18 hours ago by
Shwetha
• 0
0
votes
2
replies
104
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 1 hour ago by
Pierre Lindenbaum
161k • written 14 hours ago by
ajbarrett98
• 0
0
votes
0
replies
74
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 16 hours ago by
Ram
43k • written 23 hours ago by
naomiboldon
• 0
0
votes
0
replies
72
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
19 hours ago by
beantkapoor16
• 0
0
votes
0
replies
63
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
11 hours ago by
Christopher
• 0
0
votes
1
reply
57
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 1 hour ago by
Pierre Lindenbaum
161k • written 6 hours ago by
melissachua90
▴ 70
0
votes
1
reply
42
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
updated 1 hour ago by
Pierre Lindenbaum
161k • written 4 hours ago by
analyst
▴ 50
0
votes
0
replies
33
views
imputation through beagle
panel
beagle
reference
imputation
3 hours ago by
analyst
▴ 50
0
votes
0
replies
20
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 hours ago by
beginner123
• 0
29 results • Page
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Recent Votes
A: Trimmomatic: What is the difference between paired and unpaired output files in
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
Answer: Tissue-specific DEG analysis with DEseq2
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
Answer: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
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Recent Replies
Comment: BioLabDonkey - new Mac program for molecular biologists
by
vytarasov
▴ 180
Update of BioLabDonkey - Version 5.6 - In silico PCR function is added.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
cross posted: https://stackoverflow.com/questions/78462732/ > Please mind that posting the same question to multiple sites can be perceive…
Comment: java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
by
Pierre Lindenbaum
161k
command is missing, version is missing.
Answer: Failed to open VCF file
by
Pierre Lindenbaum
161k
> Error: Failed to open vcf file Fixing: No such file or directory one of your file is missing, obviously. Check files exist using `[…
Answer: Align paired and unpaired reads simultaneously using Bowtie2?
by
Ruqaiya
• 0
I have forward reads that didn't require any trimming except for adapter sequence. but the reverse read file required trimming so i trimmed…
Comment: Trimmomatic: What is the difference between paired and unpaired output files in
by
Ruqaiya
• 0
can we not mention unpaired ? i have a reverse read file that needs a lot of trimming but forward file is usable. I don't understand how to…
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
rackbersingh
• 0
It is an indeed an old assignment question, I am doing revision and practicing answering questions for an upcoming test and just wanted to …
Comment: How are score_weights calculated in this code?
by
carolofharvest
▴ 40
I've found this code [in this site :][1] . It doesn't seem like they've shared any additional information about this in the previous line…
Comment: Correlation Analysis
by
Researcher
▴ 30
Thank you so much. I ran based on the above code and found that all gene columns have the same values, which you obtain as the average corr…
Answer: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
use bcftools merge with --force-samples and then use jvarkit https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ to replace the no-call …
Answer: In IGV is this a heterogeneous mutation or false call?
by
swbarnes2
14k
Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
> Here's a few lines from the head of the raw fastq If your files are actually compressed (as their names suggest) then you should not be …
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
If you added the `\` before the `+` then there is no need for it. It makes it appear that the sequences are not in proper fastq format. Ple…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
Mensur Dlakic
★ 27k
This seems to be the same unanswered question as before, except that its description is split over two threads. You are now forcing us to r…
Answer: what is another word for a BLAST "hit"?
by
dec986
▴ 380
I'll probably go with "matches" even though it doesn't sound as good as just "hit"
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