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Salmon RNA-Seq transcript quantification
Salmon RNA-Seq
updated 1 hour ago by ★ 7.3k • written 3 hours ago by • 0
0
votes
0
replies
20
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Negative coverage depths when running jgi_summarize_bam_contig_depths (Metabat2)
assembly metagenome Metabat
2 hours ago by amir.rakhimov.b • 0
0
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0
replies
23
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News: Course: Comparative Genomics (ONLINE; April 7-11)
SNVs ComparativeGenomics SVs GenomeAnnotation
3 hours ago by Physalia-courses ★ 2.6k
833
votes
169
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169k
views
110 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 5 months ago by 3.4k • written 8.3 years ago by 102k
0
votes
1
reply
68
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Discrepancy in GEO2R vs. Raw Data Analysis: Significance of DEGs
Raw-Data-Analysis Microarray GEO2R Probe-IDs
updated 4 hours ago by 87k • written 8 hours ago by ▴ 10
0
votes
1
reply
93
views
DiffBind Normalization ATAC-Seq Question: When to drop a sample?
ATAC-Seq DiffBind
updated 4 hours ago by 87k • written 21 hours ago by • 0
0
votes
0
replies
50
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Advice
freelance bioinformatics job biology
9 hours ago by José • 0
0
votes
10
replies
304
views
MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genome
reference-genome
updated 1 hour ago by 165k • written 1 day ago by • 0
0
votes
0
replies
58
views
Pathways Logic
Logic Reactome Netlist
14 hours ago by sciwiseg • 0
0
votes
2
replies
171
views
CNV detection
ressources CNV Large_Cohort computation
updated 20 hours ago by ★ 4.2k • written 1 day ago by • 0
0
votes
0
replies
78
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cfRNA-seq data
cfRNA-Seq
19 hours ago by frarodmar17 • 0
0
votes
1
reply
108
views
fastq direction
bioinfo
updated 19 hours ago by 149k • written 1 day ago by • 0
1
vote
4
replies
246
views
Seeking chloroplast and mitochondrial reference for barley
barley chloroplast reference mitochondrial genome
updated 1 day ago by • 0 • written 2 days ago by ▴ 100
0
votes
0
replies
79
views
Help with Reproducing Global Bird Migration Flyway Map in R
R Flyway Map
1 day ago by Biodeer ▴ 40
7
votes
8
replies
1.4k
views
Tool: Fast, flexible grep for very large FASTQ files
grepq grep-like FASTQ
1 day ago by milesforjazz ▴ 70
1
vote
1
reply
150
views
Changing order of elements on Chord diagram in R
Chort Chart R Diagram Plot
updated 1 day ago by ▴ 330 • written 1 day ago by ▴ 70
0
votes
0
replies
106
views
advice on rooting a tree in R
R tree ggtree phylo
1 day ago by Matteo Ungaro ▴ 110
4
votes
3
replies
313
views
Using other individuals and related species to improve a de novo genome assembly
Illumina
updated 1 day ago by 4.7k • written 4 days ago by ▴ 10
0
votes
2
replies
165
views
Sankey plot for unequal node sizes
R sankey network ggplot
updated 1 day ago by 87k • written 2 days ago by ▴ 10
0
votes
0
replies
119
views
Best tools for gene regulatory netweork analysis
time-course network transcriptome RNA-seq
2 days ago by f.tomoyuki • 0
0
votes
4
replies
203
views
Pymol semaglutide structure
Pymol protein PDB Tool structure
2 days ago by Hansen_869 ▴ 80
0
votes
0
replies
98
views
Consensus Peak Shifts after dba_count() and Default Peak Width in DiffBind
DiffBind CHIP-Seq
2 days ago by Siqi • 0
0
votes
1
reply
147
views
Variant Validation Tool for Mouse RNA-seq
mouse variants transcriptome validation
updated 2 days ago by 55k • written 2 days ago by • 0
2
votes
4
replies
485
views
Ensemble Neural Network - Stacking ensemble neural network accuracy is significantly similar or low compared to base models
Neural-network Gradient-boosting Cox Random-forest Ensemble
1 day ago by Yugan Gogul Muthukumar ▴ 10
0
votes
1
reply
164
views
How to analysed RNA Seq for multiple samples
RNA-SEQ Transcriptome
updated 2 days ago by ★ 4.4k • written 2 days ago by • 0
2
votes
5
replies
276
views
Transcriptome Variant Calling Mapping to Introns
mouse introns transcriptome alignment variants
updated 2 days ago by 21k • written 3 days ago by • 0
6
votes
9
replies
397
views
How to extract a multiple sequence alignment file from a CRAM file?
samtools cram
updated 1 day ago by ★ 4.2k • written 3 days ago by ★ 2.9k
0
votes
1
reply
147
views
Can DiffBind Perform Peak Calling and Differential Analysis Directly from BAM Files?
DiffBind CHIP-Seq
updated 2 days ago by 87k • written 2 days ago by • 0
1
vote
4
replies
266
views
Dealing with UMIs
UMI
updated 1 day ago by 21k • written 2 days ago by • 0
2
votes
5
replies
290
views
Multiple factors in DESeq2
deseq2
updated 2 days ago by 21k • written 2 days ago by ▴ 30
5
votes
4
replies
282
views
Does sam 2048 flag discriminate secondary from supplementary alignments?
samtools secondary supplementary alignment
updated 3 days ago by 149k • written 3 days ago by ▴ 40
0
votes
1
reply
443
views
monocle 3-- Could not get node in small cluster
monocle3
updated 2 days ago by ★ 2.7k • written 10 months ago by ▴ 100
0
votes
0
replies
126
views
How to extract CDS from WGS data in rice?
RAP-DB CDS Genomics WGS
2 days ago by ChanderKant (CK) Chaudhary • 0
0
votes
0
replies
124
views
retrieve type translocation ,deletion, duplication with fusion RNA detection tools
fusions fusioncatcher arriba star
2 days ago by ieie ▴ 20
0
votes
6
replies
276
views
Best way to assess relatedness of eukaryotic organisms from sequencing reads?
phylogenomics phylogenetics ngs kmer sequencing
updated 2 days ago by ★ 1.5k • written 2 days ago by ▴ 30
3
votes
2
replies
192
views
Block size of SSD file storage
snp assembly ssd
updated 2 days ago by 149k • written 2 days ago by ▴ 310
1
vote
2
replies
215
views
Impact of the number of PCs on the clustering in scRNA seq
clustering pca scrna-seq
updated 2 days ago by ★ 1.4k • written 3 days ago by • 0
1
vote
2
replies
194
views
PLINK 1.07 Segmentation fault (core dumped)
PLINK
2 days ago by Alice • 0
0
votes
1
reply
160
views
Installing vg on Mac failed due to "Could not find libomp"
vg
updated 2 days ago by ▴ 730 • written 2 days ago by • 0
0
votes
0
replies
120
views
Integration of metabolomics and transcriptomic of
Metabolomics transcriptomics
3 days ago by somanin92 • 0
0
votes
0
replies
141
views
Semaglutide docked in Albumin PDB
sema Pdb semaglutide albumin
3 days ago by Hansen_869 ▴ 80
2
votes
3
replies
261
views
Forum: Career Advice
careeradvice
updated 3 days ago by 5.9k • written 3 days ago by • 0
0
votes
1
reply
156
views
Manta <DUP:TANDEM> interpretation
structural
updated 3 days ago by 165k • written 3 days ago by ▴ 560
7
votes
4
replies
475
views
Tool: AliNe (Alignment in Nextflow)
nextflow alignment
2 days ago by Juke34 9.1k
2
votes
5
replies
1.3k
views
How to completely align chromosomes/scaffolds from de novo genome assemblies using MUMMER or other tools?
visualization genome alignment
updated 3 days ago by ★ 2.9k • written 4 weeks ago by ▴ 10
0
votes
0
replies
132
views
which column to consider for venn from emapper.annotations file
emapper
3 days ago by analyst ▴ 60
0
votes
0
replies
142
views
Read length mismatch between bam and query reads
GMAP Pacbio
3 days ago by 蓝寒 • 0
0
votes
2
replies
212
views
blastp for short sequences not finding a sequence that I know is in the database
blastp short
2 days ago by ricfoz ▴ 100
0
votes
2
replies
246
views
cytoscape Stringdb identifiers can't be mapped to uniprot or ensembl
map stringdb cytoscape
2 days ago by nicole • 0
0
votes
2
replies
223
views
How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?
format question dosage hds
updated 3 days ago by 4.9k • written 4 days ago by • 0
120,654 results • Page 1 of 2414
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Recent Replies
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by Pierre Lindenbaum 165k
> samtools faidx GRCh38_full_analysis_set_plus_decoy_hla.fa chrY | md5sum AGAIN: the checksum cannot be calculated from the raw output o…
Answer: Salmon RNA-Seq transcript quantification by dsull ★ 7.3k
I'm assuming "for windows" means you're trying to install it on Windows? According to https://salmon.readthedocs.io/en/latest/building.htm…
Answer: Discrepancy in GEO2R vs. Raw Data Analysis: Significance of DEGs by ATpoint 87k
GEO2R is very primitive. I would always download raw data and process myself. That is more reproducible. Then results are what they are, gi…
Answer: DiffBind Normalization ATAC-Seq Question: When to drop a sample? by ATpoint 87k
Usually, you perform some exploration like PCA and plotting metrics like sample2sample correlation, sequencing depth etc. to see whether a …
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by GenoMax 149k
Do you need the original reads to map to the T2T genome or are you interested in the original reference to map to T2T genome. You do not ne…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by offset • 0
>That means samtools is able to find the correct reference but the one you are downloading manually is incorrect. The reference genomes G…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by GenoMax 149k
That means `samtools` is able to find the correct reference but the one you are downloading manually is incorrect. > I need to get origi…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by offset • 0
**no need to provide the -T option** remove -T option I can get include chrY records. But not I want. I need to get original fasta file …
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by offset • 0
samtools view -H HG00465/HG00465.final.cram | grep -F '@SQ' | grep chrY output: @SQ SN:chrY LN:57227415 M5:ce3e31103…
Comment: Alphafold in colab - homotrimer by sjp24 • 0
Thank you very much for replying. I did try this but I could only get it to work for one sequence, but that's OK, thanks again.
Comment: fastq direction by GenoMax 149k
You may want to do this --> https://www.biostars.org/p/179035/#179037
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by GenoMax 149k
If I recall a prior discussion right, `samtools ` should download the correct reference from Ensembl per one of the `samtools` dev/maintain…
Answer: CNV detection by cmdcolin ★ 4.2k
VCF files, just plain SNP VCF files for example, can provide several "signals" of information for detecting CNVs including - calculati…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by Pierre Lindenbaum 165k
> => no output for above command ah sorry it's @SQ not @SEQ > this is type error again, the checksum cannot be calculated from the ra…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom by offset • 0
samtools view -H HG00465.final.cram | grep -F '@SEQ' | grep chrY => no output for above command samtools faidx GRCh38_full_analysis_se…
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