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122,202 results • Page
671 of 2445
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why hisat2 mapping sam file has many sam flags
sam
RNA-seq
sequencing
hisat2
genome
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
szp770
▴ 10
0
votes
0
replies
1.9k
views
Job:
Bioinformatics Computer Systems Engineer at Berkeley Lab
systems
infrastructure
updated 2.7 years ago by
Ram
45k • written 4.6 years ago by
BerkeleyLab
▴ 70
4
votes
4
replies
3.6k
views
GATK markduplicates out of memory
Assembly
WGS
MarkDuplicates
GATK
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
williamsbrian5064
▴ 540
0
votes
1
reply
1.1k
views
Troubleshooting: rRNA depletion RNAseq no DE genes
R
RNA-seq
DESEq2
STAR
updated 4.6 years ago by
MatthewP
★ 1.4k • written 4.6 years ago by
oludhe
▴ 90
1
vote
2
replies
967
views
Does this output indicate my bam is paired end?
samtools
4.6 years ago by
curious
▴ 900
0
votes
0
replies
547
views
Individual Gene Association with GWAS SNP data
Limma
DE
GWAS
SNP
4.6 years ago by
Harrsha
• 0
2
votes
2
replies
1.7k
views
How to analyse a list of GO terms
gene ontology
4.6 years ago by
renandosreiss
▴ 10
14
votes
14
replies
4.3k
views
7 follow
Forum:
Bioinformatics startup market analysis
startup
written 4.6 years ago by
gtechbio
▴ 30
2
votes
2
replies
6.7k
views
How to count elements with a specific condition in csv file using python
code
python
csv
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
mumdooh
• 0
0
votes
1
reply
788
views
Does PLINK only deal with SNP?
PLINK
updated 4.6 years ago by
chrchang523
11k • written 4.6 years ago by
Julia_W
• 0
2
votes
4
replies
1.6k
views
Merge different VCFs from multiple individuals including singletons
VCFTools
Genomics
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
Mari
▴ 30
0
votes
2
replies
978
views
How to normalize 2 samples having 6 separate treatments
normalization
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
ntelkar
• 0
3
votes
2
replies
975
views
Phenotrex installation help
microbial
phenotrex
phenotypes
4.6 years ago by
sagrant
▴ 10
0
votes
2
replies
2.9k
views
In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?
snp
kissplice
rna-seq
stack
KisSplice
updated 4.3 years ago by
Ram
45k • written 4.6 years ago by
bioinformaticsstudent
• 0
0
votes
0
replies
973
views
Job:
[Apply by 5/23 ] PhD scholarship on functional and evolutionary genomics
evolution
long-read
PhD
genomics
4.6 years ago by
Mari
▴ 30
2
votes
2
replies
3.0k
views
How To Find Data About Tss Of Mirna?
mirna
updated 4.6 years ago by
jim_grigor
• 0 • written 14.2 years ago by
Sunflow
▴ 10
0
votes
0
replies
978
views
SVA variable of interest in eQTL analysis
sva
eqtl
4.6 years ago by
Colari19
▴ 90
1
vote
3
replies
1.5k
views
Overall mappability of genome
gem
mappability
ngs
4.6 years ago by
boczniak767
▴ 880
2
votes
4
replies
4.0k
views
enrichGO() error: unable to find an inherited method for function ‘keytypes’ for signature ‘"GRanges"’
clusterProfile
4.6 years ago by
Trinh
▴ 10
5
votes
5
replies
2.3k
views
Why is there difference FASTA file in an Accession number?
uniprot
updated 4.6 years ago by
GenoMax
154k • written 4.7 years ago by
Trinh
▴ 10
1
vote
2
replies
1.8k
views
Identify coordinates from the VCF generated from Vg call
call
vg
vgtool
4.6 years ago by
puddingmeow516
▴ 10
17
votes
21
replies
5.1k
views
8 follow
Forum:
bioinformatics thesis
thesis
updated 4.6 years ago by
Joe
22k • written 4.6 years ago by
eridanus
▴ 40
0
votes
0
replies
779
views
News:
Learn to Analyze and Visualize Microbiome Data with Nephele & MicrobiomeDB
microbiome
updated 4.6 years ago by
jared.andrews07
★ 19k • written 4.6 years ago by
karlynn.noble
▴ 60
0
votes
0
replies
690
views
How to handle mis-annotated chimeric genes?
chimeric
MAKER
curation
annotation
4.6 years ago by
liorglic
★ 1.5k
0
votes
2
replies
1.6k
views
Vg Call, not detecting SV due to soft-clipping
vgteam
vg
variation
graph
4.6 years ago by
jcmouren
• 0
0
votes
0
replies
1.7k
views
Job:
Application data scientist (f/m/d)
Computational-biology
updated 2.7 years ago by
Ram
45k • written 4.6 years ago by
ina.jaschinski
• 0
0
votes
2
replies
1.1k
views
How to covert Plot_ly codes to ggplot2 codes?
R-studio
GWAS
visualization
ggplot2
4.6 years ago by
anikcropscience
▴ 270
0
votes
3
replies
1.8k
views
I tried to compare results which I got it from DESeq2, but got this error?
DeSeq2
4.6 years ago by
arulin
• 0
2
votes
3
replies
1.2k
views
Coverage required for 3' end RNA-seq methods
cel-seq2
updated 4.6 years ago by
Carlo Yague
9.0k • written 4.6 years ago by
Aspire
▴ 390
0
votes
0
replies
666
views
How to Write same Gene name in column with strain identifier!
awk
NJ
perl
Phylogeny
updated 4.6 years ago by
benformatics
4.2k • written 4.6 years ago by
Info.shi
▴ 30
3
votes
4
replies
2.8k
views
How can I remove ligands in PDB structure?
PDB
structure
protein
4.6 years ago by
jsw940
▴ 10
1
vote
3
replies
1.9k
views
Tool/method to calculate the sequence context of variants?
sequence
context
variant
4.6 years ago by
Ian
6.1k
0
votes
0
replies
1.7k
views
Midpoint root tree specification.
tree
iqtree
phylogeny
nwk
4.6 years ago by
K.Gee
▴ 40
0
votes
0
replies
795
views
Issue with PDB+chain to Pfam mapping and domain filter
Pfam
mapping
PDB
python
4.6 years ago by
jmungar2
▴ 10
2
votes
4
replies
1.2k
views
Indexing
0-based
index
1-based
4.6 years ago by
GG
• 0
0
votes
0
replies
617
views
Whole Metagenome Analysis of resistome dataset
metagenomics
ngs
4.6 years ago by
hafiz.talhamalik
▴ 350
5
votes
13
replies
4.6k
views
How to calculate percent coverage of each read for nanopore
alignment
nanopore
sequencing
4.6 years ago by
sonsunjirachote
• 0
0
votes
0
replies
712
views
How to correct single nucleotide variation due to PCR bias ?
datacorrection
rstudio
nucleotide
merge
4.6 years ago by
Gautier
• 0
3
votes
2
replies
1.6k
views
Multiple sequence alignment tools
sequence
Multiple
alignment
updated 4.6 years ago by
Joe
22k • written 4.6 years ago by
Acapmiolo
▴ 20
2
votes
2
replies
4.2k
views
Scatter plot of DEG in R
R
RNA-seq
Bioconductor
DEG
4.6 years ago by
ATCG
▴ 410
3
votes
0
replies
977
views
How to use IDBA-UD to perform scaffolding on assembled contigs?
IDBA-UD
assembly
MEGAHIT
scaffolds
contigs
4.6 years ago by
Rui
▴ 50
0
votes
1
reply
971
views
Compare 2 VCF files A & B and return TRUE for every A variant in B, FALSE otherwise
compare
vcf
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
felixm
▴ 40
0
votes
4
replies
1.1k
views
Transcriptome Analysis
RNA-seq
Illumina
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.6 years ago by
harpreet.kaur
• 0
0
votes
0
replies
587
views
ICGC library information
rnaseq
4.6 years ago by
camelbbs
▴ 710
0
votes
1
reply
1.1k
views
Using ClueGO without generating a network
Visualization
ClueGO
updated 4.6 years ago by
ashish
▴ 680 • written 4.6 years ago by
henriquechapola
• 0
0
votes
2
replies
1.4k
views
Display alignment BAM file
IGV
Alignment
display
RNA-seq
updated 4.6 years ago by
gglim
▴ 220 • written 4.6 years ago by
adnan.lahuf
• 0
2
votes
1
reply
866
views
Intersecting Wald DESeq2 Results
LRT
DESeq2
Wald
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
lucia.liu54
• 0
0
votes
0
replies
1.5k
views
UK Biobank methylation data
DNA
biobank
methylation
4.6 years ago by
Ivan
• 0
6
votes
5
replies
1.8k
views
How to create matrix from row data
sed
perl
R
awk
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
Info.shi
▴ 30
0
votes
1
reply
2.5k
views
How to interpret Enrichr combined score 'infinity' value
Enrichr
Enrichment
updated 14 months ago by
mazegriff
▴ 100 • written 4.6 years ago by
srs204
• 0
122,202 results • Page
671 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets
by
GenoMax
154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
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