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GATK is throwing an error when using dbsnp hg19 or GCRCh 38 build 156
and dnsp156.40 dbsnp build156.25
updated 8 months ago by 166k • written 8 months ago by • 0
6
votes
3
replies
1.8k
views
Cattle reference genome ARS-UCD2.0
cow genome assembly
updated 8 months ago by 56k • written 8 months ago by ▴ 60
0
votes
1
reply
650
views
RNA-seq WGCNA anlysis
Rna-seq WGCNA
updated 8 months ago by 89k • written 8 months ago by ▴ 10
0
votes
0
replies
457
views
Splitting single cell data
ScRNA
8 months ago by otieno43 ▴ 40
0
votes
0
replies
629
views
News: Online course - Flow cytometry data analysis with R/Bioconductor
R Bioconductor Flow-Cytometry Cancer-Genomics
6 months ago by Physalia-courses ★ 2.6k
0
votes
0
replies
622
views
Help selecting WGCNA soft thresholding power
POWER WGCNA SOFT
updated 8 months ago by 3.9k • written 8 months ago by • 0
0
votes
0
replies
614
views
Deciding Between TOIL Processed Data (Xena) vs. TCGA Biolinks Data for DE Analysis
DESeq TCGA Xena RNA-Seq BIOLINKS
8 months ago by lyan125 ▴ 10
0
votes
1
reply
879
views
working with shapeit.
shapeit
updated 9 months ago by • 0 • written 18 months ago by • 0
1
vote
1
reply
829
views
rRNA contamination in RNASeq fdata
contamination rRNA RNASeq
updated 9 months ago by ★ 7.7k • written 9 months ago by ▴ 70
0
votes
2
replies
876
views
inserting Normalized count data
DESeq2
updated 9 months ago by 89k • written 9 months ago by ▴ 10
2
votes
5
replies
1.5k
views
high IgG background
background IgG signal cuttag
updated 8 months ago by 89k • written 9 months ago by ▴ 30
0
votes
2
replies
960
views
Unexpected results: Conservation of cCREs
ccres genes encode conservation
8 weeks ago by Yacob • 0
4
votes
3
replies
1.7k
views
FastQC polyA and polyG trimming in RNA-seq
polyA QC trimming RNA-seq Fastq
8 months ago by joonhong kwon ▴ 70
2
votes
4
replies
1.4k
views
Finding Orthologs in Unannotated Genomes
orthologs
9 months ago by triplee0305 ▴ 20
4
votes
4
replies
1.3k
views
Differential Expression for a predefined one or multiple genes and multiple testing
Deseq2 Multiple-testing Differential-Expression
updated 8 months ago by ★ 8.3k • written 9 months ago by • 0
2
votes
0
replies
20k
views
Herald: The Biostar Herald for Monday, December 23, 2024
herald
9 months ago by Biostar 3.6k
0
votes
6
replies
2.6k
views
dbSNP and indels
VCF
updated 9 months ago by ▴ 20 • written 2.7 years ago by • 0
0
votes
1
reply
910
views
Retrieve query start and end positions on reverse strand with Pysam
python alignment Pysam
updated 9 months ago by ★ 1.7k • written 9 months ago by ▴ 10
1
vote
0
replies
1.4k
views
Job: Looking for Internship/Junior Bioinformatics Opportunity
Opportunities Bioinformatics
9 months ago by Felix ▴ 10
0
votes
0
replies
500
views
Seeking Tool for Transcription Factor Motif Enrichment Analysis on RRBS Dataset
RRBS Epigenetics Transcription-Factors DNA-Methylation Motif-Enrichment
updated 9 months ago by 45k • written 9 months ago by ▴ 20
0
votes
2
replies
1.1k
views
can we perform separate channel analysis of two-channel Agilent microarray data?
two-channel microarray
9 months ago by Bini • 0
0
votes
0
replies
509
views
Finding Similar Subsequences From Protein Sequences
Pfam HMMER Protein BLAST
9 months ago by jet • 0
3
votes
2
replies
899
views
Can different genes encode the same proteins?
UniProt genes proteins enzymes
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
0
votes
3
replies
1.0k
views
Stingtie error: the input alignment file is not sorted
.SAM .BAM .GTF Stringtie
updated 9 months ago by 166k • written 9 months ago by • 0
1
vote
1
reply
787
views
edgeR customized normalization for differential analysis
voom CPM normalization edgeR DGE
updated 9 months ago by 89k • written 9 months ago by • 0
0
votes
3
replies
967
views
scRNA - Illumina naming convention unclear
scRNA
updated 9 months ago by 153k • written 9 months ago by • 0
1
vote
1
reply
653
views
Help finding error in fasta file
fasta
updated 9 months ago by 45k • written 9 months ago by • 0
0
votes
8
replies
1.9k
views
How to get Normal Samples from TCGA?
Normal TCGA
updated 8 months ago by ★ 1.3k • written 9 months ago by ▴ 30
1
vote
3
replies
1.2k
views
Challenges Using KING for Relatedness Analysis with Non-Standard Genomes (8000 Chromosomes)
VCF Relatedness
8 months ago by alex • 0
0
votes
0
replies
457
views
Assessment of upstream/downstream variants
downstream_variant variant_annotation Upstream_variant
9 months ago by Nesma • 0
2
votes
1
reply
788
views
STARsolo sorted bam contains 'non-whitelisted' barcodes
starsolo alignment
updated 9 months ago by ★ 7.7k • written 9 months ago by ▴ 310
0
votes
0
replies
630
views
News: I created an NGS data analysis tutorial site (ngs101.com)!
NGS Tutorial RNA-seq
updated 9 months ago by 153k • written 9 months ago by ▴ 300
2
votes
5
replies
1.2k
views
Wrong SNP calling in my bcftools output
snp bcftools vcf vcftools
8 months ago by pablo ▴ 350
0
votes
0
replies
606
views
How to Convert Ensembl Gene and Transcript IDs to RefSeq mRNA and Gene IDs from isoforms data?
R biomaRt refseq ensembl
9 months ago by mauricio.1313 • 0
0
votes
1
reply
818
views
How to annotate all SNPs from a BAM file, not just the variants?
Annotation SNP BAM Variant-Calling
updated 9 months ago by ★ 1.7k • written 9 months ago by ▴ 40
0
votes
4
replies
1.2k
views
Manually modified gtf cannot be loaded into featureCounts STAR
gtf subread featurecounts star
updated 9 months ago by 153k • written 9 months ago by • 0
3
votes
3
replies
1.1k
views
Computational way to distinguish between polyA and total RNA bulk RNA-seq
RNA-seq
9 months ago by predeus ★ 2.1k
1
vote
2
replies
1.2k
views
How to use artemis comparison tool?
artemis ACT comparison genomics
updated 9 months ago by 153k • written 9 months ago by ▴ 760
1
vote
0
replies
600
views
News: Cellosaurus release 51
cellosaurus knowledgebase biocuration cell-line
updated 9 months ago by 45k • written 9 months ago by ▴ 140
0
votes
3
replies
1.9k
views
News: Last Day: Special Deal - 15% Off - RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
Transcriptomics splicing differential-expression RNA-Seq
9 months ago by ecSeq Bioinformatics ▴ 20
2
votes
5
replies
1.7k
views
Non Variant Sites in GVCF File
GATK VCF SNP
updated 9 months ago by 23k • written 9 months ago by ▴ 10
3
votes
8
replies
1.5k
views
How to make .fasta file
.fasta file
9 months ago by otieno43 ▴ 40
0
votes
0
replies
430
views
The VCF generated by the pan-genome contains missing values due to conflicts
VG MC
9 months ago by chiyong4783 • 0
3
votes
3
replies
1.1k
views
Understanding BWA parameters
BWA
updated 9 months ago by ★ 1.7k • written 9 months ago by ▴ 20
2
votes
1
reply
826
views
Bonferroni correction for burden by transcripts
Association-test statistics
updated 9 months ago by ★ 8.3k • written 9 months ago by ▴ 540
6
votes
3
replies
1.6k
views
featureCounts problems with GTF generated by myself
featureCounts GTF
updated 9 months ago by 153k • written 2.2 years ago by ▴ 60
1
vote
2
replies
704
views
Prokka Error
Prokka
updated 9 months ago by ★ 30k • written 9 months ago by • 0
0
votes
0
replies
480
views
CLIPdb bulk download all RBP binding sites with annotations.
bindingdata RBP bulkdownload CLIPdb
9 months ago by ttcheau • 0
0
votes
0
replies
484
views
Maftools and MutationalPatterns tools
maftools MutationalPatterns
updated 9 months ago by 45k • written 9 months ago by • 0
0
votes
2
replies
871
views
Interpret IGV
flags IGV read
9 months ago by najim3 • 0
121,908 results • Page 45 of 2439
Recent Votes
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
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Recent Replies
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
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