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1,000 results • Page 3 of 20
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4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 10 months ago by 43k • written 9.5 years ago by • 0
4
votes
6
replies
349
views
Protein loops
protein Loop
7 weeks ago by Curious ▴ 10
4
votes
14
replies
1.2k
views
remove white space in fastq file
fastq
updated 4 months ago by 142k • written 4 months ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
4 days ago by anna ▴ 20
4
votes
16
replies
1.8k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 10 weeks ago by 43k • written 7 months ago by • 0
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by 87k • written 8 months ago by • 0
4
votes
3
replies
496
views
Parsing columns with awk
awk
updated 6 months ago by 43k • written 6 months ago by ▴ 300
4
votes
11
replies
677
views
Remove X in row name with only number
GSVA
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 260
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 12 weeks ago by ▴ 10 • written 3.4 years ago by ▴ 60
4
votes
7
replies
1.5k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 142k • written 9 months ago by • 0
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid software-error autogrid4
updated 11 months ago by 43k • written 3.2 years ago by • 0
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 750
4
votes
7
replies
778
views
Alternative for grep in a for loop
linux
updated 6 months ago by 43k • written 6 months ago by ▴ 20
4
votes
3
replies
737
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
11 months ago by Dan ▴ 180
4
votes
4
replies
806
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 11 months ago by 21k • written 11 months ago by ▴ 20
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 10 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
4
votes
8
replies
614
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
4
votes
1
reply
574
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
ClusterProfiler RNA-seq GSEA
updated 9 months ago by ★ 1.6k • written 9 months ago by ▴ 100
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
4
votes
6
replies
853
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 4 weeks ago by 43k • written 5 months ago by ▴ 30
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex illumina sequencing
updated 4 months ago by 142k • written 4 months ago by ▴ 120
4
votes
6
replies
939
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by ★ 2.4k • written 11 months ago by • 0
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
4
votes
4
replies
375
views
Average expression of a sample in single-cell data
single-cell rna-seq
4 weeks ago by newuser2024 • 0
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 11 months ago by • 0 • written 20 months ago by ▴ 20
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq transcriptome SRA
updated 10 months ago by 82k • written 10 months ago by • 0
4
votes
5
replies
1.2k
views
STAR mapping - regarding output files content
STAR RNA-seq mapping
updated 8 months ago by ▴ 900 • written 8 months ago by • 0
4
votes
6
replies
1.1k
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
updated 6 months ago by ▴ 120 • written 7 months ago by ▴ 130
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 50
4
votes
3
replies
766
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
8 months ago by stefano.iantorno ▴ 70
4
votes
3
replies
709
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
2
replies
647
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 6 months ago by ★ 1.5k • written 6 months ago by ▴ 100
4
votes
4
replies
655
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
8 months ago by nshenoy ▴ 50
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness how_are_we_stranded_here leafcutter bash
updated 6 months ago by 20k • written 8 months ago by • 0
4
votes
4
replies
615
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 142k • written 8 months ago by ★ 2.9k
4
votes
3
replies
321
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 12 weeks ago by 4.6k • written 12 weeks ago by ▴ 30
4
votes
9
replies
596
views
variant calling
variant-calling
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 11 months ago by 43k • written 4.6 years ago by ▴ 120
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 5 weeks ago by 43k • written 5.6 years ago by ▴ 110
4
votes
7
replies
582
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 20 days ago by 43k • written 21 days ago by ▴ 20
4
votes
1
reply
1.8k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 8 months ago by ★ 2.4k • written 8 months ago by ▴ 120
4
votes
3
replies
399
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 11 weeks ago by 142k • written 11 weeks ago by ▴ 20
4
votes
5
replies
542
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 142k • written 9 months ago by • 0
4
votes
7
replies
806
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 260
4
votes
6
replies
1.0k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python fastq
9 months ago by eorr ▴ 30
4
votes
3
replies
604
views
Identifying enhancers that regulate certain genes
enhancers
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 40
4
votes
2
replies
245
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 29 days ago by 161k • written 29 days ago by • 0
4
votes
7
replies
1.1k
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by 4.6k • written 7 months ago by ▴ 20
1,000 results • Page 3 of 20
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Recent Replies
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
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Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme by e.r.zakiev ▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ by GenoMax 142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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