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121,999 results • Page 619 of 2440
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3
votes
8
replies
2.8k
views
Query for limma and DEseq2
deseq2 limma
updated 2.7 years ago by 45k • written 4.3 years ago by ▴ 20
0
votes
0
replies
737
views
Data Visualization tool for mutations difference between primary and metastatic tumor.
metastasis visualization wgs varscan2 mutations
4.3 years ago by moustafa_abohawya ▴ 30
2
votes
4
replies
2.7k
views
How to set the number of mismatch in blastn
blastn mismatch penalty
updated 4.2 years ago by 22k • written 4.3 years ago by • 0
0
votes
4
replies
1.3k
views
Finding all pathogens for a disease
database Textmining
4.3 years ago by tra.0831 • 0
0
votes
0
replies
1.1k
views
annotating regions with annotate Peak and ucsc refGene gives different answers in some cases
gene_names r ngs annotate
4.3 years ago by pt.taklifi ▴ 70
0
votes
0
replies
738
views
How to show that one docking is better than another with Pymol visually
docking structure pymol pdb
4.3 years ago by gundalav ▴ 380
0
votes
1
reply
1.1k
views
Snakemake error with blast
Blast cd Snakemake
4.3 years ago by kamanovae ▴ 100
0
votes
0
replies
612
views
Docking
gromacs autodock docking
updated 2.9 years ago by 45k • written 4.3 years ago by • 0
4
votes
2
replies
1.3k
views
DESeq2: impact of number of expressed genes in differential expression analysis
genes number of DESeq2 expressed
4.3 years ago by mbk0asis ▴ 700
0
votes
0
replies
610
views
Prompt doesn’t autocomplete with tab key
mothur autotab
4.3 years ago by Mario • 0
0
votes
1
reply
3.0k
views
HMMCopy readcounter
readcounter ichorCNA CNV HMMcopy
updated 4.3 years ago by 154k • written 4.5 years ago by ▴ 120
3
votes
3
replies
1.8k
views
separate multi-alleles from bi-alleles
genetics population
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 180
0
votes
1
reply
772
views
COVID 19 analysis workflow
Workflow COVID19
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
1
vote
3
replies
2.0k
views
ClustalW using Biopython
clustalw biopython fasta fastq
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 20
0
votes
0
replies
658
views
What is the appropriate Limma design matrix for the interaction between sex and age?
r microarray limma
4.3 years ago by lintek08 • 0
0
votes
2
replies
1.0k
views
Code output inconsistency
codon python
updated 2.6 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
537
views
PDB and corresponding gene ID/ nucleotide sequence database
PDB gene
4.3 years ago by dnlburns808 • 0
0
votes
1
reply
3.6k
views
DESeq2 results function not working
differential expression bioconductor R
updated 4.3 years ago by ★ 19k • written 4.3 years ago by • 0
3
votes
14
replies
3.8k
views
Trouble getting BLAT to work
Blat
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 10
3
votes
5
replies
1.7k
views
Opposing expression profiles in the same WGCNA module
clustering WGCNA
4.3 years ago by cfourps ▴ 10
18
votes
24
replies
7.1k
views
6 follow
Free to use bioinformatics servers & large memory
Server
updated 4.2 years ago by 45k • written 4.3 years ago by ▴ 70
15
votes
21
replies
21k
views
10 follow
gff3 to CDS fasta
genome sequence gff3
updated 4.3 years ago by ▴ 260 • written 8.9 years ago by ▴ 50
0
votes
1
reply
900
views
Copy number alteration prediction from DNA-seq
dataset Genomic DNAseq gene CNA
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
0
replies
744
views
Do I need to include the "ins:me:alu" line for my MR analysis
Randomization Mendelian data stat GWAS Summary
4.3 years ago by paria ▴ 110
2
votes
2
replies
3.2k
views
How Should I Deal with Paired-End Shotgun Metagenomic Reads for DIAMOND Analysis?
diamond metagenomics megan paired-end
updated 4.3 years ago by 35k • written 4.3 years ago by ▴ 10
2
votes
6
replies
3.7k
views
7 follow
Handling manhattan plots in vector graphics editors
snp SNP R
updated 4.3 years ago by ★ 3.1k • written 7.1 years ago by ▴ 20
0
votes
4
replies
1.7k
views
Lexogen Quantseq Mapping Rates with Salmon
Quantseq RNAseq Salmon Lexogen Mapping
4.2 years ago by abnerapsley • 0
0
votes
0
replies
629
views
Increase in discordant alignments with Bowtie2 after changing trimming stringency?
cutadapt trimgalore ATAC-seq stringency bowtie2
4.3 years ago by uli • 0
1
vote
2
replies
1.9k
views
small RNA-Seq analysis and doubts
nc RNA-Seq small miRNA-Seq
4.3 years ago by Sergio • 0
2
votes
2
replies
1.3k
views
merging paired ends illumina reads without quality with Pear
pear merging illuminareads
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
0
votes
1
reply
759
views
How to get all the metabolic pathways present within a bacteria species?
database
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 250
0
votes
0
replies
778
views
News: Online training - Introduction to Deep Learning in biology
DeepLearning
4.3 years ago by Physalia-courses ★ 2.6k
5
votes
2
replies
7.6k
views
TPM to log2(TPM+1)
log TCGA KIRC RNA-seq TPM
4.3 years ago by David ▴ 30
1
vote
1
reply
1.6k
views
Downloading the RefSeq proteins complete data set
ftp refseq
updated 4.3 years ago by 154k • written 4.3 years ago by ★ 2.9k
2
votes
2
replies
2.3k
views
How to write the rule for Indexing with bowtie2-build and Expand function in snakemake ?
bowtie2 snakemake indexing
updated 4.3 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
556
views
Autodock4
Autodock4
updated 2.6 years ago by 45k • written 4.3 years ago by • 0
0
votes
6
replies
2.0k
views
tool to identify genomic structural variations in completely sequenced prokaryotic genomes
prokaryotes genomic variations mugsy structural
updated 4.2 years ago by ▴ 600 • written 4.3 years ago by • 0
0
votes
2
replies
2.2k
views
Imputation of X chromosome non-PAR for male subjects
SNP imputation X chromsoome
4.1 years ago by Apprentice ▴ 190
0
votes
1
reply
1.0k
views
defining input files for SeqIO
SeqIO python
updated 4.3 years ago by ▴ 650 • written 4.3 years ago by • 0
3
votes
1
reply
802
views
Annotating an assembly according to alignment against a reference genome
genbank annotation alignment
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 70
0
votes
1
reply
843
views
Degenerate Primer Sequence Recovery
python degenerate-primers
updated 2.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
1
reply
3.5k
views
BL21 vs BL21 Star
E.coli BL21
updated 2.6 years ago by 45k • written 4.3 years ago by ▴ 170
0
votes
0
replies
767
views
snpeff effect prediction confusion
variant hgvs snpeff annotation
4.3 years ago by najoshi ▴ 30
0
votes
2
replies
978
views
Chip seq data related query
values Chip data narrowPeak intensity
4.3 years ago by sujasubramanian ▴ 70
0
votes
4
replies
1.9k
views
Issues with genome indexing with bowtie2-build
bowtie2 index
updated 4.3 years ago by 5.3k • written 4.3 years ago by • 0
9
votes
13
replies
5.8k
views
error when running bbduk
bbduk
updated 15 months ago by 45k • written 4.3 years ago by ★ 1.3k
9
votes
6
replies
3.9k
views
Trouble running snakemake while defining maximum RAM usage
snakemake
updated 4.3 years ago by 15k • written 4.3 years ago by ★ 1.2k
0
votes
0
replies
651
views
KEGG pathway analysis of miRNA in rice(oryza sativa)
target kegg pathway miRNA prediction
4.3 years ago by Aswini • 0
1
vote
3
replies
1.5k
views
CURL UniprotIDs not working consistently
curl uniprot python bash
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
0
votes
0
replies
637
views
How to divide reads mapping to two different genes using featureCounts
featureCounts mapping alignment rna-seq
4.3 years ago by Apex92 ▴ 320
121,999 results • Page 619 of 2440
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Recent Replies
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Billy Rowell ▴ 510
Is there a reason you'd like to use IPA over, for instance, hifiasm? I'd recommend starting with hifiasm. For pbipa, try downgrading to s…
Answer: Active site using castpfold by dthorbur ★ 3.1k
This is very similar to your recent [post](https://www.biostars.org/p/9615406/) - if you aren't going to provide the protein example for a …
Answer: Differences between published differential gene expression results and own analy by Zhenyu Zhang ★ 1.3k
1. When you said "the same dataset", are you sure about the files are the same, or you just mean the same list of patients? There are many …
Comment: downloading raw bam files from pacbio sequencer by Arup Ghosh 3.4k
Try: https://www.google.com/search?q=site:https://downloads.pacbcloud.com/public/dataset/+%22subreads%22
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
If they are not available at PacBio site then your chances of getting them are going to be significantly reduced. Only other source may be …
Comment: downloading raw bam files from pacbio sequencer by pranavdatar01 • 0
Yes, I did check. They don't have any.
Comment: downloading raw bam files from pacbio sequencer by pranavdatar01 • 0
I want to download the HDF5 .bax.h5 files or BAM/SAM .subreads.[bs]am files which out from the pacbio sequencer. Are there any sample demo …
Comment: installation of package ‘DESeq2’ had non-zero exit status by GenoMax 154k
> Installation paths not writeable, unable to update packages Are you a normal user on a system administered by other admins?
Comment: installation of package ‘DESeq2’ had non-zero exit status by lieven.sterck 16k
Hi https://www.biostars.org/u/151679/ welcome to the forum. Quite an extensive post but I can't seem to find a real question? Please don…
Comment: Pseudogene - scarce info by mf810 • 0
That's actually a huge help, thank you so much! Even if the finding is there's no relevant findings, it's nice to have someone else check…
Answer: Transverse data by basu • 0
Sounds like you’ve got a data party going on—too many duplicates crashing it! If you need a quick fix for those pesky repeats, maybe check …
Answer: Pseudogene - scarce info by Mensur Dlakic ★ 30k
> The gene plays a pivotal role in some pathways of the immune response, but tbh I could'nt find any mention of my pseudogene on the linked…
Answer: SNP calling ONT sequenced files by cfos4698 ★ 1.2k
My personal preference is using [clair3][1]. I'm unsure if CLC didn't work because your compute resources are too limited, or if there are …
Comment: HIV NL4-3 transcriptome fasta by Ales ▴ 50
Hi, Wanted to update here that full transcriptome annotations for thousands of hiv genomes (including NL4-3) are now available at https://…
Answer: HIV NL4-3 transcriptome fasta by Ales ▴ 50
You can get full transcriptome annotation for the NL4-3 genomes: https://ccb.jhu.edu/HIV_Atlas/11676/AF324493.2 . Note the accession ID tho…
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