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122,037 results • Page 2 of 2441
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1
vote
4
replies
559
views
Problems with PacBio's Improved Phased Assembler (IPA)
pacbio hifi assembly genome
7 days ago by Panos ★ 1.8k
0
votes
6
replies
615
views
downloading raw bam files from pacbio sequencer
raw bam_file raw_subreads reads
updated 8 days ago by 154k • written 9 days ago by • 0
0
votes
0
replies
286
views
Best way to map biological pathways to cancer hallmarks using PLMs (without building models)?
PLM mapping LLM extraction Relation
8 days ago by DEPANSHI • 0
1
vote
2
replies
624
views
installation of package ‘DESeq2’ had non-zero exit status
Bioinformatics
updated 8 days ago by 154k • written 8 days ago by • 0
0
votes
1
reply
335
views
Checkm results differ from database info
Checkm
updated 4 days ago by 45k • written 8 days ago by • 0
0
votes
2
replies
1.2k
views
Transverse data
EXCEL Unix
updated 8 days ago by • 0 • written 2.7 years ago by • 0
0
votes
0
replies
278
views
Is this the correct order of steps in GATK germline cohort variant calling (VQSR workflow)?
gVCF VCF GATK VQSR
8 days ago by Ramnaresh • 0
0
votes
0
replies
296
views
How to select background metabolite sets for differential metabolite enrichment analysis?
enrichment ORA
8 days ago by Edward • 0
1
vote
3
replies
475
views
Pseudogene - scarce info
pseudogene mastersdegree
updated 5 days ago by 89k • written 9 days ago by ▴ 10
1
vote
4
replies
1.9k
views
HIV NL4-3 transcriptome fasta
rna-seq CLIP-seq
updated 9 days ago by ▴ 90 • written 5.5 years ago by ▴ 140
1
vote
1
reply
369
views
Doubt on docking
docking active site bioinformatics
updated 9 days ago by ★ 30k • written 9 days ago by • 0
1
vote
0
replies
279
views
News: Online course: RNA sequencing data analysis using R and Bioconductor - 3–14 November
R DifferentialExpressionAnalysis RNAseq Bioconductor
9 days ago by Physalia-courses ★ 2.7k
6
votes
3
replies
483
views
Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
fastqc nextflow multiqc
updated 9 days ago by ★ 1.5k • written 10 days ago by ▴ 30
0
votes
1
reply
5.1k
views
News: ::Last Call:: In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 in Munich) - BS-Seq, ChIP-Seq, ATAC-Seq, ...
chip-seq atac-seq bs-seq
9 days ago by ecSeq Bioinformatics ▴ 20
0
votes
2
replies
5.7k
views
Best set of tools / workflows for predicting the biosynthesis pathways of complex organic molecules
ngs pathways bioinformatics
updated 10 days ago by ▴ 100 • written 25 days ago by ▴ 60
12
votes
15
replies
3.6k
views
6 follow
Tools to simulate Illumina short read sequences and ONT long reads with a reference genome
simulate reads bioinformatics short short-read
1 day ago by PolenP ▴ 10
1
vote
1
reply
353
views
Corresponding BAM files
BAM SRA GEO FASTQ
updated 10 days ago by 154k • written 10 days ago by ▴ 130
0
votes
2
replies
1.8k
views
Analyzing CRISPR and RNAi genome wide screens
CRISPR RNAi meta analysis
updated 10 days ago by ▴ 250 • written 7.3 years ago by ▴ 280
0
votes
3
replies
2.8k
views
meta data analysis for clustering
meta-analysis clustering functional genomics
updated 10 days ago by ▴ 250 • written 7.7 years ago by ▴ 230
2
votes
9
replies
3.5k
views
GTF file for HIV strain pNL4-3
HIV annotation mapping
updated 10 days ago by ▴ 90 • written 7.3 years ago by ★ 1.9k
0
votes
1
reply
313
views
Diffbind or DESEQ2 Chipseq data
Chipseq DESEQ2 Diffbind
5 days ago by Irene • 0
0
votes
0
replies
270
views
Job: Postdoctoral Fellowship at the American Museum of Natural History's Richard Gilder Graduate School
Postdoctoral Fellowship
10 days ago by Info-rggs ▴ 20
0
votes
0
replies
265
views
News: Autumn School in Bioinformatics - online, 20–24 October
NGS Phylogenomics RNAseq Singularity Docker
10 days ago by Physalia-courses ★ 2.7k
1
vote
4
replies
605
views
Dorado in PowerShell on Windows
Windows on PowerShell in Dorado
updated 9 days ago by ★ 19k • written 10 days ago by ▴ 10
1
vote
0
replies
284
views
Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
gatk
10 days ago by curious ▴ 900
1
vote
4
replies
563
views
Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2 or winnowmap?
winnowmap minimap2 R10.4.1 Nanopore
10 days ago by tungsega ▴ 10
2
votes
2
replies
440
views
Nextflow: How to format input tuple for STAR_ALIGN process with STAR index directory
nextflow
11 days ago by DdogBoss ▴ 30
4
votes
4
replies
543
views
how to respond that my research does not have experimental validation
rebuttal
updated 11 days ago by ★ 30k • written 11 days ago by ▴ 40
6
votes
7
replies
756
views
Quantification using salmon in alignment-based mode after minimap2 run
nanopore ont salmon
3 days ago by Assa Yeroslaviz ★ 1.9k
1
vote
1
reply
368
views
infercnv error at STEP 18 - file descriptor is too large for select()
R 10x singlecell infercnv
11 days ago by yura.grabovska ▴ 850
0
votes
0
replies
253
views
News: online course - Environmental Metagenomics
Illumina Metagenomics Nanopore MAGs
11 days ago by Physalia-courses ★ 2.7k
0
votes
1
reply
308
views
Need Help : JGI IMG Bulk Download
Bioinformatics
updated 11 days ago by 154k • written 11 days ago by • 0
0
votes
4
replies
456
views
How to convert gff to Sequin format with gff3-to-tbl?
genome annotation conversion Sequin gff
updated 12 days ago by 154k • written 12 days ago by ▴ 770
0
votes
1
reply
445
views
How much coverage is needed for high-quality phylogenetic and admixture analyses using short-read WGS in plants?
coverage
updated 10 days ago by 8.0k • written 12 days ago by • 0
1
vote
10
replies
3.1k
views
Collect COV file by BedCoverage
copynumbervariation ClinCNV ngs
updated 4.3 years ago by ★ 3.0k • written 4.3 years ago by ▴ 20
0
votes
1
reply
326
views
gnomad par region variants
region variant par gnomad
updated 13 days ago by 4.2k • written 14 days ago by ▴ 60
0
votes
2
replies
402
views
Forum: Help with Ideathon
PGS PRS brainstorming genomics bioinformatics
13 days ago by V K • 0
2
votes
2
replies
437
views
Gene expression equivalent of polygenic risk score ?
expression gene
14 days ago by Picasa ▴ 690
0
votes
1
reply
501
views
Help interpreting BLASTn results and phylogenetic tree for genetics practical
student
updated 15 days ago by 154k • written 16 days ago by • 0
0
votes
0
replies
281
views
News: Introduction to CRISPR for Ecology and Evolution Studies (13–16 Oct, online)
GenomeEditing Cas9 CRISPR Evolution
15 days ago by Physalia-courses ★ 2.7k
0
votes
2
replies
473
views
tximport error (medianLengthOverIsoform)
DTU RNA-seq tximport
10 days ago by LGG • 0
0
votes
8
replies
862
views
Errors with RSEM/bowtie2
RNA-seq bowtie2 RSEM Trinity
11 days ago by Olivia • 0
3
votes
1
reply
672
views
With 10x Visum HD : How to map the barcode id to the barcode sequence ?
10x barcode Visium
16 days ago by sacha ★ 2.5k
0
votes
0
replies
327
views
Job: Genetics for Biodiversity Conservation Korea - Ecuador
Ecuador biodiversity Korea
updated 15 days ago by 8.0k • written 16 days ago by • 0
0
votes
1
reply
433
views
help with modkit on nanopore sequencing data.
mokit nanopore help
updated 15 days ago by 3.9k • written 16 days ago by • 0
1
vote
0
replies
348
views
News: FastTrack Bioinformatics - Online Course in Bioinformatics
handbook biostar
16 days ago by Istvan Albert 103k
3
votes
1
reply
857
views
Dictys refuses to use CUDA supported pytorch during installation
python conda gpu
17 days ago by zwjiang ▴ 30
0
votes
0
replies
594
views
Haploview LD plot unespected results
Haploview SNPs
17 days ago by chiuni2308 • 0
0
votes
0
replies
664
views
News: online course: Efficient Data Analysis with data.table in R - 8 October
R Programming DataTable
17 days ago by Physalia-courses ★ 2.7k
1
vote
0
replies
674
views
Tool: Modernized RNA-MuTect pipeline for tumor-only RNA-seq somatic variant calling
somatic rna-seq
17 days ago by darklings ▴ 590
122,037 results • Page 2 of 2441
Recent Votes
Answer: High Variability when Peak Calling with SEACR
A: Get chromosome sizes from fasta file
How to keep the top hits only in the output file of hmmscan?
A: How to keep the top hits only in the output file of hmmscan?
ProbeID to Gene Symbol Mapping in Microarray data analysis using R
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
Answer: Choosing enrichment analysis tool
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Answer: DE analysis in nascent RNA Seq based on intron sequences by dsull ★ 7.7k
Yes, that’s fine; I don’t see why nascent transcripts should be treated differently than mature transcripts in DE analysis.
Comment: High Variability when Peak Calling with SEACR by RD ▴ 30
Hi Jared, I’m trying to figure out the right parameters to use with MACS3 for CUT&RUN data. My understanding is that it’s best to convert t…
Answer: SNP calling ONT sequenced files by Момчил ▴ 10
Yes, one can say that ONT reads do still have higher error rates in comparison to Illumina short reads, but the situation has improved sign…
Comment: MOuse Testis Enhancer region by GenoMax 154k
That web site is off-line for everyone. You will have to look for an alternate option.
Answer: Is there a way to produce/convert nhmmer output to a bed file? by colindaven 8.0k
To make it a bit clearer for nhmmer specifically, I used the following. This is code used in nextflow. # run nhmmer nhmm…
Comment: reference-guided assembly tools for short read data? by lieven.sterck 16k
there are several options to choose from, doing a quick google search will give you a lot. The main thing to keep in mind is to choose one …
Comment: Python deconvolution tools for bulk RNA-seq data by Arup Ghosh 3.4k
Check the [Bulk2Single][1] option from [OmicVerse][2] framework. [1]: https://omicverse.readthedocs.io/en/latest/Tutorials-bulk2single/…
Comment: reference-guided assembly tools for short read data? by michael.ante ★ 4.0k
I don't know how well it works for plants, but I worked with [Saute][1] and it was doing well for reference based assemblies. [1]: http…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by ATpoint 89k
Most likely a download artifact. First I would re-download and inly if that fails again then do repairing. ftp is primitive, it's just hit …
Answer: Python deconvolution tools for bulk RNA-seq data by ATpoint 89k
Imo you are approaching this the wrong way. R packages for deconvolution that are heqavily used and cited do exist, for example MuSiC and B…
Comment: MOuse Testis Enhancer region by Bioinformatics_16 • 0
@genomax Do you have access to this list? If so, could you please share it? I need it urgently.
Comment: HDOCK Server Error! by Jannatul Ferdous • 0
Tried that but unfortunately, the problem still persists :( Thanks for your response though!
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq by LChart 5.1k
While Himar1 inserts in TA motifs, the library is generated following restriction enzyme treatment (Mmrl) and ligation. The Mmrl sequence i…
Comment: Is it possible to do standard GSEA in R? by mbramble • 0
See discussion at https://support.bioconductor.org/p/9142651/#9142680 concerning issues with preranked gsea.
Comment: BWA-MEM with an array of files by LChart 5.1k
For solution 1, because bwa streams the data, you can save some space by using a named pipe: ```bash mkfifo Sample_23/concat.R1.fq.gz find…
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