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122,202 results • Page 679 of 2445
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6
votes
2
replies
1.9k
views
How to rename/replace the multiline fasta subsequence header in a fasta file?
DNA alignment fasta RNA
4.6 years ago by sunnykevin97 ▴ 1000
3
votes
5
replies
3.1k
views
Intall MAGIC-BLAST in Ubuntu from BASH SHELL in windows powershell.
magicblast ncbi ubuntu linux powershell
updated 5.2 years ago by 154k • written 5.2 years ago by • 0
0
votes
4
replies
2.1k
views
Mutect2 vcf.stats file missing
GATK mutect2 vcf.stats
updated 4.6 years ago by 45k • written 4.6 years ago by • 0
1
vote
3
replies
2.3k
views
BWA mem or samtools have any parameter to filter the mismatch reads？
mapping samtools reads BWA
4.6 years ago by Damon_Wan • 0
4
votes
1
reply
1.7k
views
Uniprot Retrieve/ID mapping
Uniprot Mapping PDB2Uniprot
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
2
votes
7
replies
3.9k
views
CNVkit detected CNV number
CNVKit copynumbervariation cnr
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 40
1
vote
2
replies
1.2k
views
igv track auto scaling fails in batch mode
igv
updated 4.6 years ago by 154k • written 4.8 years ago by • 0
0
votes
0
replies
1.2k
views
Error running MutSigCV: "missing mutation_type_dictionary_file"
error MutSigCV mutation type
4.6 years ago by alizee.diatchenko • 0
0
votes
0
replies
827
views
Negative homozygosity rates from plink --check-sex?
plink allosomes sex-check gwas
4.6 years ago by krassowski.michal ▴ 180
3
votes
7
replies
2.0k
views
How to download via biopython (proteom or genome) individual or random organisms?
genom proteom
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 30
8
votes
4
replies
3.5k
views
gzip: merged.fastq.gz not in gzip format
RNAseq
4.6 years ago by Kai_Qi ▴ 130
5
votes
1
reply
4.4k
views
1000 genomes project reference panel - GRCh38
GRCh38 build38 1KG reference_panel
updated 4.6 years ago by 2.9k • written 4.6 years ago by ▴ 130
1
vote
2
replies
1.9k
views
GATK no "SB" annotation after GenotypeGVCFs
gatk strandbias
4.6 years ago by wang.yiguan ▴ 10
0
votes
2
replies
1.2k
views
Converting tab character file to a tab delimited file
Linux
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 30
4
votes
6
replies
3.2k
views
Is number after "LOC" genes equal to its Entrez id ?
NCBI gene LOC
4.6 years ago by takoyaki ▴ 120
2
votes
3
replies
2.5k
views
Fragment length of paired-end data
paired-end
updated 4.6 years ago by 16k • written 4.6 years ago by ▴ 10
1
vote
0
replies
1.2k
views
Job: 2 PhD Scholarships in Bioinformatics in ancient sedimentary DNA and microbial DNA
metagenomics phd ancientdna sedadna ngs
4.6 years ago by Gabriel R. ★ 2.9k
1
vote
5
replies
2.1k
views
How to sort multi columns on long dataframe in R
data.frame Order R dplyr plyr
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by ▴ 270
2
votes
20
replies
7.7k
views
Converting Braker2 gtf output to gff then genbank
annotation
4.6 years ago by robert.murphy ▴ 110
3
votes
1
reply
2.0k
views
Canu transcriptome assembly behavior
nanopore RNA-Seq canu
updated 4.6 years ago by ▴ 30 • written 4.8 years ago by ▴ 80
1
vote
1
reply
1.9k
views
Calculate P-value and FDR-adjusted P-value on normalized data
RPPA P-value FDR
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 10
2
votes
5
replies
2.3k
views
How to solve multiple CDS features with same locus tag in EMBL format
annotation embl
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 110
0
votes
4
replies
1.9k
views
Separate colors in immunohistochemical staining
image python
4.6 years ago by salvatore.raieli2 ▴ 90
0
votes
4
replies
2.7k
views
remove variable sites from vcf that only differ from reference.
vcf
updated 4.6 years ago by ▴ 170 • written 4.6 years ago by ▴ 60
2
votes
1
reply
3.1k
views
How to make consensus sequence from aligned reads ?
sequence Transcriptome aligned consensus reads
4.6 years ago by Info.shi ▴ 30
0
votes
0
replies
805
views
error when imputing for mismatch legend file
impute2 haps shapeit legend
4.6 years ago by raalsuwaidi ▴ 110
0
votes
2
replies
3.8k
views
Error in FUN(left, right) : non-numeric argument to binary operator in RStudio
rstudio
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
0
replies
801
views
How do I quickly run through all possible merger outputs?
unix emboss merger
4.6 years ago by lzbenicmi • 0
3
votes
3
replies
4.4k
views
Deeptools, ComputeMatrix and plotProfile
plotprofile ComputeMatrix deeptools Average
updated 4.6 years ago by • 0 • written 4.6 years ago by ▴ 20
2
votes
1
reply
711
views
How to merge SRRs from 1 sample
analysis NGS
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
1
vote
2
replies
2.4k
views
Where to install latest Affymetrix Power Tools?
affymetrix
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 60
2
votes
9
replies
25k
views
7 follow
HISAT error: Encountered internal HISAT2 exception (#1)
RNA-Seq
updated 4.6 years ago by • 0 • written 8.5 years ago by ★ 1.5k
0
votes
0
replies
906
views
STAR - stringtie procedure
rnaseq AS stringtie splicing STAR
4.6 years ago by Hojn ▴ 30
1
vote
2
replies
917
views
Sources of gene expression levels in different tissue types
expression
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
3
votes
3
replies
3.8k
views
Do I need to download any specific adapters for Illumina small RNA sequencing kit?
Adapter trimming small RNA trimmomatic cutadapt
updated 4.6 years ago by 154k • written 8.7 years ago by ▴ 370
4
votes
3
replies
2.9k
views
Deseq2 time interaction term
deseq2 rna-seq DE R
updated 3.4 years ago by ★ 1.3k • written 4.6 years ago by ▴ 30
1
vote
1
reply
1.5k
views
calculate area under curve for profile plot (deepTools)
plotProlfile deepTools
updated 4.6 years ago by 105k • written 4.6 years ago by ▴ 20
1
vote
8
replies
3.5k
views
Prinseq lite data preprocessing
Prinseq-lite RNA-seq
updated 2.7 years ago by 45k • written 4.9 years ago by ▴ 60
1
vote
10
replies
3.0k
views
big loss after markduplication
MarkDuplicates Re-sequencing Picard
updated 4.6 years ago by ▴ 170 • written 4.6 years ago by ▴ 300
0
votes
13
replies
8.0k
views
Trimmomatic-0.36 not finding adapter directory
Directory Trimmomatic ILLUMINACLIP
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
4
votes
4
replies
1.9k
views
How comes scRNAseq linear batch corrected data looks worst than before correction?
rescalebatches regressbatches singlecell batch
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 10
0
votes
2
replies
2.0k
views
No annotation peaks when running homer
homer peaks tss
4.6 years ago by Lila M ★ 1.3k
1
vote
0
replies
1.1k
views
Parallel haplotyping
gVCF GATK HaplotypeCaller merge parallel
4.6 years ago by Poshi ▴ 10
0
votes
0
replies
823
views
How to map human variant to correspoding knock-allele in mouse
HMDC mouse MGI functional_assay knock-in
4.6 years ago by Damianos P. Melidis ▴ 60
0
votes
2
replies
1.7k
views
How to include the metadata when we build the txDb object?
txdb r
4.6 years ago by qwesxadzc9 • 0
1
vote
2
replies
999
views
question when using topgo
terms go incomplete
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
2
votes
1
reply
981
views
Convert genotypes format '12' to ACTG format
r dplyr
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 20
1
vote
3
replies
1.5k
views
How to get GO terms to specific to perticular biological process
GO Enrichment RNA-seq
updated 4.6 years ago by ▴ 140 • written 4.6 years ago by ▴ 10
1
vote
15
replies
5.2k
views
How to perform multiple alignment using MAFFT?
genome alignment gene sequence
4.6 years ago by anikcropscience ▴ 270
1
vote
3
replies
1.5k
views
How to obtain FDR across all regions investigated in DiffBind
DiffBind
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 20
122,202 results • Page 679 of 2445
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Comment: low quality data or file name swapping -- cellranger arc errors when processing
Comment: low quality data or file name swapping -- cellranger arc errors when processing
A: Regarding Microarray Platforms
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
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…
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