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388 results • Page 1 of 8
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8
votes
25
replies
1.9k
views
construction of a database
sql noSQL neo4j database
updated 5 days ago by 38k • written 22 months ago by ▴ 20
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard SAM
updated 4 days ago by 38k • written 4.6 years ago by ▴ 670
0
votes
16
replies
1.4k
views
How to convert ncbi gff file to ensembl gff format
bcftools gff
updated 5 days ago by 38k • written 7 months ago by ▴ 10
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 4 days ago by 38k • written 4.6 years ago by ▴ 670
1
vote
15
replies
1.2k
views
Samtools merge Illumina and PB bam file empty
Illumina samtools Bam PacBio
updated 4 days ago by 38k • written 2.6 years ago by • 0
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta vcf genbank gff
updated 4 days ago by 38k • written 4.5 years ago by ▴ 670
2
votes
12
replies
523
views
how to get to a VCF from bam files
Mpileup Samtools BAM bcftools VCF
updated 2 days ago by 38k • written 4 days ago by • 0
0
votes
12
replies
1.5k
views
bedtools intersect issue
bed bedtools
updated 4 days ago by 38k • written 4.6 years ago by ▴ 120
6
votes
11
replies
737
views
Calculate RPKM
RPKM
6 days ago by Chris ▴ 70
0
votes
9
replies
1.5k
views
Microarray analysis in R - target.txt,file,Sample info
R
updated 4 days ago by 38k • written 18 months ago by ▴ 10
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf bcftools
updated 4 days ago by 38k • written 3.2 years ago by ▴ 90
0
votes
9
replies
3.2k
views
Viral integration with RNA-seq data
ngs RNA-seq
updated 3 days ago by 38k • written 5.5 years ago by ▴ 570
2
votes
9
replies
1.9k
views
SAM file quality check without converting into BAM
Alignment SAM
updated 4 days ago by 38k • written 3.8 years ago by • 0
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 6 days ago by 38k • written 8.0 years ago by ▴ 10
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq pySCENIC loom
updated 5 days ago by 38k • written 7 months ago by • 0
3
votes
8
replies
290
views
getting coding exon information from Ensembl API
Ensembl API
updated 4 days ago by 38k • written 4 days ago by ▴ 30
1
vote
7
replies
1.7k
views
Is anybody experiencing problems downloading from the SRA?
SRA
updated 3 days ago by 38k • written 2.4 years ago by ▴ 90
0
votes
7
replies
1.6k
views
File format for HGMD pro file flat
variant-analysis HGMD annovar
updated 4 days ago by 38k • written 4.2 years ago by ▴ 960
2
votes
7
replies
775
views
Import data for igraph using R
r igraph
updated 5 days ago by 38k • written 12 months ago by • 0
1
vote
7
replies
857
views
Splitting BED file by technical replicate or extract all unique barcodes
BED
updated 4 days ago by 38k • written 2.7 years ago by • 0
4
votes
7
replies
2.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 4 days ago by 38k • written 21 months ago by ▴ 70
1
vote
7
replies
1.7k
views
Platypus variantcaller.c:16971 errpr
platypus
updated 6 days ago by 38k • written 4.2 years ago by ▴ 40
0
votes
7
replies
1.1k
views
Unable to convert from sam to bam file.
bam sam samtools
updated 5 days ago by 38k • written 14 months ago by • 0
1
vote
7
replies
1.1k
views
Bulk download tomato RNA or cDNA sequences (partial) with genomic loci list
SGN tomato
updated 3 days ago by 38k • written 5.0 years ago by ▴ 10
2
votes
6
replies
1.0k
views
GFF3 TO GTF CONVERSION
GFF3 Hydra GFF GTF
updated 5 days ago by 38k • written 14 months ago by • 0
1
vote
6
replies
951
views
problem for comparing 2 type of annotation file
gencode RNA-Seq TCGA
updated 3 days ago by ▴ 750 • written 4.8 years ago by ▴ 160
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services java
updated 5 days ago by 38k • written 7.8 years ago by ▴ 170
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure splign
updated 5 days ago by 38k • written 6.4 years ago by ▴ 160
2
votes
6
replies
312
views
bioinformatics problems solved by graphs data structure
Graph algorithm data-structure
updated 3 days ago by 38k • written 3 days ago by • 0
1
vote
6
replies
1.0k
views
gff file
GFF UNIPRTOT
updated 4 days ago by 38k • written 18 months ago by ▴ 10
5
votes
6
replies
2.9k
views
Changes log2FC values of DESeq2
log2FC DESeq2
updated 3 days ago by 38k • written 5.3 years ago by ▴ 30
0
votes
6
replies
1.1k
views
Raw data for chromosome 21
WCS bam sequencing
updated 4 days ago by 38k • written 4.0 years ago by • 0
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed coverage gene
updated 4 days ago by 38k • written 16 months ago by ▴ 10
0
votes
5
replies
491
views
BAM file became smaller after merging
BAM
updated 5 days ago by 38k • written 11 months ago by • 0
0
votes
5
replies
950
views
Problem with normalization by bcftools
vcf bcftools samtools
updated 4 days ago by 38k • written 2.9 years ago by ▴ 20
0
votes
5
replies
780
views
Inquiry related to vcf file and formatting
vcf bcftools
updated 4 days ago by 38k • written 19 months ago by ▴ 140
1
vote
5
replies
1.5k
views
Post alignment using RseQC
alignment RNA-Seq RSeQC
updated 3 days ago by 38k • written 5.5 years ago by ▴ 570
1
vote
5
replies
1.2k
views
Star index generation - 'std::bad_alloc' error
STAR
updated 6 days ago by 38k • written 2.2 years ago by • 0
0
votes
5
replies
3.7k
views
reading CELfiles for Human Exon 1.0 ST Array [CDF: HuEx-1_0-st-v2,coreR3,A20071112,EP]
CEL RNA-Seq software-error R
updated 4 days ago by 38k • written 6.8 years ago by ▴ 30
0
votes
5
replies
329
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq scRNA-seq single-cell genomics ngs
updated 5 days ago by 127k • written 6 days ago by ▴ 650
1
vote
5
replies
1.8k
views
igv_plotter error, I cannot run igv_plotter on my BAM file, RuntimeError: Xvfb did not start
visualisation bam igv_plotter igv
updated 4 days ago by 38k • written 5.7 years ago by ▴ 350
1
vote
5
replies
324
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R row_split ComplexHeatmap
updated 5 days ago by ▴ 710 • written 5 days ago by • 0
0
votes
5
replies
841
views
Problems with consensus fasta
bed bcftools samtools
updated 4 days ago by 38k • written 16 months ago by ▴ 80
1
vote
5
replies
2.2k
views
Where can I download chromatin state genomic co-ordinates of C.elegans ?
c.elegans chromatin-states
updated 2 days ago by 38k • written 8.4 years ago by ★ 1.5k
0
votes
5
replies
2.5k
views
Recoding plink file from 12 to 01
plink plink2chromopaiter.pl
updated 3 days ago by 38k • written 5.2 years ago by ▴ 20
2
votes
5
replies
558
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 5 days ago by 13k • written 9 days ago by ▴ 30
1
vote
4
replies
351
views
Loading Traitdata file for WGCNA analysis
R WGCNA
updated 5 days ago by 38k • written 5 months ago by ▴ 50
3
votes
4
replies
262
views
Creating sample groups from a combination of genes for survival analysis
Survival
4 days ago by krushnach80 ★ 1.1k
0
votes
4
replies
1.1k
views
How to download FASTA file from psRNAtarget
FASTA sequence
updated 2 days ago by 38k • written 4.8 years ago by • 0
0
votes
4
replies
1.4k
views
How to colour points in cnetplot of clustprofiler?
clusterprofiler cnetplot R
updated 2 days ago by • 0 • written 19 months ago by ▴ 20
388 results • Page 1 of 8
Recent Votes
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Recent Replies
Answer: Installing rlang version 1.1.0 by Lluís R. ★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
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