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694 results • Page 3 of 14
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3
votes
6
replies
773
views
Ciriquant not configuring hisat2 indexed files
ciriquant
29 days ago by Atul K. • 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 12 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
8
votes
5
replies
6.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
1
vote
5
replies
375
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 3 days ago by ★ 2.0k • written 4 days ago by • 0
1
vote
5
replies
662
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 27 days ago by • 0 • written 4 months ago by • 0
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 8 days ago by • 0 • written 6.7 years ago by • 0
1
vote
5
replies
506
views
How should I make kallisto indexes?
kallisto
updated 21 days ago by ★ 6.0k • written 5 weeks ago by ▴ 150
1
vote
5
replies
332
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq deseq2
updated 4 days ago by 43k • written 4 days ago by • 0
2
votes
5
replies
523
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 6 days ago by 43k • written 12 days ago by • 0
5
votes
5
replies
366
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 18 days ago by ▴ 40 • written 18 days ago by ▴ 150
0
votes
5
replies
407
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 17 days ago by 10k • written 17 days ago by ▴ 750
0
votes
5
replies
296
views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated 5 days ago by 142k • written 6 days ago by • 0
0
votes
5
replies
352
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
7 days ago by SilhouetteQ • 0
2
votes
5
replies
555
views
Marking duplicates using UMIs
Deduplication UMI
updated 29 days ago by 19k • written 4 weeks ago by • 0
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 4 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
5
votes
5
replies
681
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 17 days ago by • 0 • written 26 days ago by ★ 3.9k
1
vote
5
replies
813
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
0
votes
5
replies
315
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 12 days ago by 21k • written 13 days ago by • 0
2
votes
5
replies
555
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
22 days ago by ashaneev07 ▴ 20
4
votes
5
replies
467
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
22 days ago by analyst ▴ 50
0
votes
5
replies
210
views
Why most genes have high padj values
RNA-seq DEG
updated 17 hours ago by 43k • written 1 day ago by • 0
2
votes
5
replies
962
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 21 days ago by ★ 2.0k • written 2.1 years ago by • 0
0
votes
5
replies
449
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 25 days ago by 142k • written 26 days ago by ▴ 90
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
6 days ago by Arton ▴ 10
1
vote
5
replies
233
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos atacseq
updated 5 days ago by 161k • written 5 days ago by ▴ 50
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 29 days ago by 43k • written 10.6 years ago by ▴ 150
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 12 days ago by • 0 • written 5.1 years ago by ★ 1.8k
1
vote
5
replies
276
views
Annotating file using bcftools
annotation plink bcftools
4 days ago by kl ▴ 10
1
vote
5
replies
414
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 13 days ago by 54k • written 14 days ago by • 0
0
votes
5
replies
439
views
Telescope issue
Telescope RNA-seq
updated 19 days ago by 142k • written 20 days ago by • 0
2
votes
5
replies
292
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 7 days ago by 8.5k • written 7 days ago by • 0
1
vote
5
replies
386
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 14 days ago by 43k • written 15 days ago by • 0
1
vote
5
replies
488
views
HCL database download
HCL
updated 13 days ago by 43k • written 17 days ago by ▴ 20
3
votes
5
replies
420
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
17 days ago by Maverick ▴ 10
0
votes
5
replies
471
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 23 days ago by 100k • written 27 days ago by ▴ 10
0
votes
5
replies
440
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
26 days ago by njornet ▴ 20
0
votes
5
replies
362
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
8 days ago by feather-W • 0
2
votes
5
replies
436
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
25 days ago by Lada ▴ 30
1
vote
5
replies
525
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
27 days ago by anasjamshed ▴ 120
0
votes
5
replies
339
views
how to treat the replicates while performing WGCNA
clustering WGCNA replicates
12 hours ago by mavy ▴ 10
1
vote
5
replies
410
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
18 days ago by Riccardo ▴ 10
3
votes
5
replies
651
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
29 days ago by n_navy • 0
5
votes
5
replies
351
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
13 days ago by Chris ▴ 280
3
votes
5
replies
365
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 28 days ago by 142k • written 29 days ago by • 0
2
votes
5
replies
609
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 8 days ago by ▴ 40 • written 17 days ago by ▴ 30
0
votes
5
replies
363
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
12 days ago by me • 0
0
votes
5
replies
313
views
calculating genomic coverage/ base overlap in R
genomics
updated 2 days ago by ★ 1.2k • written 5 days ago by • 0
2
votes
5
replies
447
views
Importing a fastq file
Fastq
updated 11 days ago by ▴ 120 • written 12 days ago by • 0
3
votes
5
replies
357
views
Generating mpileup file using samtools
mpileup samtools
updated 17 days ago by 21k • written 18 days ago by • 0
0
votes
5
replies
461
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 18 days ago by ▴ 200 • written 18 days ago by • 0
694 results • Page 3 of 14
Recent Votes
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
A: Where to find PCR duplicate reads in bam file?
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
A: Bcftools merge taking too much time and producing large file
Answer: Kraken2 database
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Recent Replies
Comment: What is the amount of sequencing data produced annually? by Mohamed • 0
Here's a more neat version of the plot generated while writing my dissertation: ![enter image description here][1] [1]: https://raw.gi…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
what a pity...
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Yes, I can. But there are only two factors that affect my data PCA distribution: groups and donor. And the rest is regarded as residual. …
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by colindaven 6.4k
Please delete this as it has nothing to do with the topic of this forum, bioinformatics. Thanks
Comment: Add stats to the plot by marco.barr ▴ 130
if don't work try binding the stats without group. stat_data4 <- data4.ts %>% ungroup() %>% t.test(data = ., value ~ Cond…
Comment: Nextflow docker: Error response from daemon by Pierre Lindenbaum 161k
you should ask : https://github.com/nf-core/sarek/issues/
Comment: Where to find old version of GATK best practice by Pierre Lindenbaum 161k
https://github.com/gatk-workflows ?
Comment: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
Hi, if you can please post a separate question with inputs and expected output, reply here with a link to it, and I'll take a look.
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Hi again Alex, sorry to ask another question about this, but how can I tweak this code to keep **all** of the SNPs that pass the threshold …
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Hello I have a quick question, I did as you said , and further added the traits, found the correlation among the modules and the traits us…
Comment: Elbow plot question (scRNA seq data analysis - scanpy tutorial) by ojaswinipandey • 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial) by Dave Carlson ★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds by marco.barr ▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool by Ram 43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by Ram 43k
This post does not fit the theme of this forum.
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