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Forum: Basic beginner bioinformatics for biochemistry for university first year students
books course
updated 4.5 years ago by 12k • written 4.5 years ago by • 0
0
votes
5
replies
2.1k
views
Comparing two bai files
BAM BAI
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 90
0
votes
0
replies
770
views
How to print the best matching hit while making a BLAST search? / BioPython
biopython blast best_hit_overhang max_hpsp hit
4.5 years ago by sezer.sevin • 0
4
votes
3
replies
4.3k
views
How do I count the real total reads from a fastq file?
NGS Fastq End Paired Sequencing
updated 3.7 years ago by ▴ 110 • written 4.5 years ago by ▴ 10
1
vote
7
replies
2.6k
views
Basic annotation of refseq bacterial genomes
annotation bacteria
4.5 years ago by biobiu ▴ 150
2
votes
4
replies
2.1k
views
Subsampling reads
metagenome metagenomics microbial
4.5 years ago by amy ▴ 20
5
votes
4
replies
4.0k
views
Difference between Meta'omics and Multi'omics
Omics
updated 4.5 years ago by ▴ 180 • written 4.5 years ago by ▴ 250
0
votes
0
replies
932
views
trmap alternative for gffcompare?
GffCompare Novel-Transcripts StringTie RNA-Seq
4.5 years ago by SKY ▴ 60
1
vote
2
replies
2.2k
views
How to extract subset of protein structure (PDB format) file based on a subsequence of protein
protein pdb python r
updated 4.5 years ago by ▴ 390 • written 4.5 years ago by ▴ 380
4
votes
1
reply
3.3k
views
Does HaploView perform phasing?
HaploView Phasing PHASE fastPHASE Haplotypes
updated 4.5 years ago by ▴ 20 • written 8.7 years ago by ▴ 150
0
votes
0
replies
969
views
Novel transcript class code GffCompare?
Novel-Transcripts GffCompare RNA-Seq
4.5 years ago by SKY ▴ 60
1
vote
2
replies
3.4k
views
Spatial transcriptomics data
seurat scanpy no-visium .h5 spatial
4.5 years ago by lsudupe ▴ 30
4
votes
4
replies
7.6k
views
Installing samtools version 1.12
samtools
updated 4.4 years ago by 105k • written 4.5 years ago by ▴ 90
0
votes
0
replies
874
views
how to install non-condo dependency and add it to .yaml env file?
snakemake
4.5 years ago by AnnaS • 0
0
votes
0
replies
741
views
tRNA fragment
RNA-seq small
4.5 years ago by 972050141 • 0
0
votes
0
replies
698
views
Is there a simple script to identify plasmid Inc or Rep type given its DNA sequence?
inc rep plasmid
4.5 years ago by crisstyl ▴ 10
1
vote
1
reply
1.2k
views
Is there is a way to know that the sra data I'm interested in has a bad fastqc from sra database on ncbi before downloading it or before making fastq…
fastq fasta SRA
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 20
16
votes
1
reply
4.6k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ★ 90k
1
vote
1
reply
1.3k
views
Lowly undergrad has trouble finding good primers for Professor!
intron primerblast primerdesign ncbi exon
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
0
replies
965
views
How to change various SNP identifiers into rsID in Plink.
Chromosome SNP position Plink rsid
4.5 years ago by geno89 ▴ 20
1
vote
1
reply
985
views
Normalize RiboTag samples to input before differential expression with DESeq2
RiboTag DESeq2 RNA-Seq Differential Expression Analysis
updated 3.8 years ago by • 0 • written 4.5 years ago by ▴ 10
0
votes
3
replies
2.0k
views
Unable to extract country name from genbank file
Genbank data extraction
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by • 0
0
votes
2
replies
1.3k
views
Extraction of specific sequences from a FASTA file
Genomics
4.5 years ago by aranyak111 • 0
9
votes
7
replies
13k
views
6 follow
Forum: When applying to a PhD program in Harvard or MIT, how many publications are recommended?
GradSchool Grad Harvard School Application
updated 4.3 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
597
views
How can I upload pan-genome database data to Neo4j?
pantools pan-genome Neo4J
4.5 years ago by vyacheslavshumbar • 0
0
votes
4
replies
1.5k
views
How to download the final reads of SRA data from NCBI using fastq-dumb
fastq fasta SRA
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 20
1
vote
3
replies
3.2k
views
Download and install StringTie
StringTie RNA-Seq
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 60
0
votes
0
replies
637
views
Gene ontology analysis on viral proteins
gene go ontology
4.5 years ago by Chvatil ▴ 140
0
votes
0
replies
475
views
Can anyone suggest me how to perform recombination analysis using RDP4 software
RDP4
4.5 years ago by tilakvallabhaneni • 0
0
votes
1
reply
1.1k
views
Extract data from GTF file
gtf java
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
3
votes
4
replies
1.5k
views
Pair-End Sequencing Algorithm Confusion (Illumina)
Sequencing
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 110
0
votes
1
reply
1.0k
views
How does Control freec compute for the X and Y chromosomes
CNC freec Control variation Copy
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
3
votes
2
replies
1.6k
views
Is the number of spots in SRA equal to the number of reads
fastq fasta SRA
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 20
0
votes
3
replies
1.3k
views
Can you lose unmapped reads in BAM file?
unmapped reads BAM
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by • 0
2
votes
2
replies
1.4k
views
Example of simple repository using htslib API to read in .bcf
htslib
4.5 years ago by 4galaxy77 2.9k
0
votes
3
replies
5.7k
views
Can someone suggest the tool to Calculate Tumor Mutation Burden from VCF file
VCF tumor-mutational-burden R TMB
updated 2.4 years ago by 45k • written 7.1 years ago by • 0
10
votes
6
replies
5.5k
views
Limma: Extracting results when the global option of the decideTests is used
R limma
updated 3.3 years ago by ★ 1.3k • written 4.7 years ago by ▴ 130
2
votes
5
replies
1.8k
views
MERLIN: skipped due to megabytes problem
software error SNP snp
updated 4.4 years ago by ▴ 10 • written 4.9 years ago by • 0
1
vote
4
replies
2.4k
views
problem with plotheatmap colors
colors deeptools plotheatmap
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
3
replies
1.2k
views
Very low number of micro RNA reads
Genomics
updated 4.5 years ago by 23k • written 4.5 years ago by • 0
0
votes
3
replies
1.4k
views
CD45R isoforms in RNA-seq
RNAseq
4.5 years ago by dioscorea.bulbifera ▴ 10
4
votes
2
replies
1.3k
views
How to measure the similarity of operons from two species?
operon similarity bacteria
updated 4.5 years ago by ▴ 30 • written 5.6 years ago by ▴ 180
0
votes
2
replies
1.3k
views
Subset gff with non-unique seqid
gff
4.5 years ago by hazirliver ▴ 10
4
votes
6
replies
2.8k
views
python importing featureCounts to automate multiple files
featureCounts python
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
930
views
classification or metadata for metabolites
annotations
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 90
12
votes
6
replies
3.4k
views
Which is better: PacBio or Illumina for de novo transcriptome?
transcriptome PacBio Illumina
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 40
0
votes
1
reply
1.3k
views
what is the best tool to remove PCR duplicates from miRNA seq without UMI?
mirna-seq sequencing
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 320
0
votes
2
replies
1.3k
views
topGO : compare 2 distinct groups
topGO
3.5 years ago by lagartija ▴ 160
2
votes
2
replies
4.8k
views
dyld : Library not loaded: Reason: image not found
python dyld R
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 20
1
vote
3
replies
1.8k
views
How to remove repeated sequence region in Interproscan .gff3 with many ORFs?
format region interproscan gff3 gtf
updated 4.4 years ago by 9.3k • written 4.5 years ago by • 0
122,199 results • Page 644 of 2444
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Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
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Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
You can check the read lengths of each file to determine which one is the R1 and which is the R2. Also, check the 10x protocol version they…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
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