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1,000 results • Page 5 of 20
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8
votes
13
replies
2.5k
views
Issue about install Cutadapt in ubuntu1404
cutadapt
7.2 years ago by Joe ▴ 30
8
votes
8
replies
2.5k
views
6 follow
Blast Is Giving Me A Result Totally Unrelated To The Gene I Expect
blast primer
updated 10.9 years ago by 20 • written 11.1 years ago by • 0
8
votes
9
replies
3.0k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq duplication fastqc
updated 23 months ago by ▴ 870 • written 4.5 years ago by ★ 2.1k
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 5.7 years ago by 44k • written 8.3 years ago by ▴ 50
8
votes
8
replies
1.9k
views
Sequence alignment algorithm for big size genes in MATLAB
alignment Matlab next-gen
7.0 years ago by r.tor ▴ 50
8
votes
6
replies
2.4k
views
Using Bandage to finish ambiguous long-read assembly?
Assembly Bandage long reads Unicycler
updated 5.3 years ago by 20 • written 5.4 years ago by ★ 2.0k
8
votes
11
replies
2.0k
views
using STAR instead of HISAT2
STAR
updated 22 months ago by 44k • written 22 months ago by ▴ 280
8
votes
10
replies
2.0k
views
FASTA of translated amino acid sequences in their six reading frames, which one is the optimal?
aminoacid protein peptide Reading optimal frames
2.8 years ago by Luis999 ▴ 20
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
8
votes
9
replies
3.1k
views
error in rstudio
csv matrix rstudio
updated 20 months ago by 44k • written 8.8 years ago by ★ 4.3k
8
votes
1
reply
1.2k
views
CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
CalculateGenotypePosteriors gatk trio ped
3.3 years ago by DareDevil ★ 4.3k
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
6.3 years ago by Sharon ▴ 610
8
votes
11
replies
5.0k
views
Increasing kmer limit in SPAdes
Assembly Bacterial Spades Velvet
7.8 years ago by rrcutler ▴ 120
8
votes
11
replies
3.6k
views
Semantic Similarity selection in REVIGO: which is better? many clusters or few?
go revigo gene ontology
6.5 years ago by Farbod ★ 3.4k
8
votes
7
replies
6.0k
views
Download human 3 UTR FASTA file
genome
8.2 years ago by bharata1803 ▴ 560
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq differential expression
4.6 years ago by guillaume.rbt ★ 1.0k
8
votes
30
replies
5.3k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 4.2 years ago by ▴ 560 • written 4.2 years ago by ▴ 20
8
votes
12
replies
4.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 14 months ago by 44k • written 2.8 years ago by ▴ 30
8
votes
25
replies
3.1k
views
construction of a database
sql noSQL neo4j database
updated 14 months ago by 44k • written 3.0 years ago by ▴ 20
8
votes
11
replies
2.0k
views
Sending files to Galaxy
Galaxy fastq
7.7 years ago by statfa ▴ 760
8
votes
5
replies
3.2k
views
7 follow
What is the best way to merge multiple fasta files containing contigs?
Assembly Anvi’o fasta
updated 5.3 years ago by 11k • written 5.3 years ago by • 0
8
votes
8
replies
1.8k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq DEseq2
updated 3.1 years ago by ▴ 390 • written 3.1 years ago by • 0
8
votes
7
replies
4.3k
views
ORF finder script
orf open reading frame bash shell sequencing
7.4 years ago by ahm3dhany ▴ 20
8
votes
6
replies
5.7k
views
miRanda output meaning?
rna-seq
updated 7.0 years ago by 47k • written 7.0 years ago by ▴ 40
8
votes
7
replies
4.1k
views
Error with Bowtie 2
bowtie2 alignment
6.9 years ago by valerie ▴ 100
8
votes
5
replies
915
views
Why some genome assemblies don't have annotation?
genome assembly
5.1 years ago by 860101959 ▴ 10
8
votes
4
replies
2.0k
views
using different tools to identify differential exprssed genes
rna-seq RNA-Seq R
updated 20 months ago by 44k • written 8.7 years ago by ▴ 20
8
votes
6
replies
4.4k
views
Bwa Aln -Q 15 When To Use It? What Does It Do?
bwa trimming
updated 11.8 years ago by 100k • written 11.8 years ago by ▴ 640
8
votes
5
replies
1.7k
views
differential expression analysis with DESeq2 & edgeR
RNA-Seq
3.5 years ago by Rob ▴ 170
8
votes
4
replies
3.2k
views
How to use machine learning in Fastq/Fasta data?
machine learning fasta fastq sequencing
7.0 years ago by inkprs ▴ 70
8
votes
5
replies
3.6k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM FASTQ
updated 17 months ago by 44k • written 8.9 years ago by ▴ 60
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.5 years ago by • 0 • written 6.9 years ago by ▴ 140
8
votes
8
replies
1.6k
views
Clustering DNA sequences (from human genome)
sequencing genome
4.7 years ago by abdul.karim • 0
8
votes
7
replies
1.3k
views
grep with -f switch is not working
grep
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 30
8
votes
14
replies
2.5k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
2.9 years ago by johnsonqinz • 0
8
votes
5
replies
1.0k
views
Why could we infer a physical time scale (e.g. a billion year) from a phylogenetic analysis?
phylogeny phylogenetic tree
4.6 years ago by johnnytam100 ▴ 110
8
votes
11
replies
5.8k
views
RNASeq gender identification
RNA-Seq
6.7 years ago by popayekid55 ▴ 110
8
votes
6
replies
1.2k
views
I have 2 identical jupyter notebooks and I get BiomartException when I run one but not the other.
biomart python
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 50
8
votes
20
replies
2.7k
views
Getting read depth for normal and tumour
R WGS vcf
5.1 years ago by zizigolu ★ 4.3k
8
votes
11
replies
4.1k
views
STAR can not detect this chimeric read
RNA-Seq fusion STAR
updated 7.5 years ago by 20 • written 7.7 years ago by 11k
8
votes
7
replies
607
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by 44k • written 3 months ago by ▴ 100
8
votes
7
replies
3.9k
views
6 follow
Compatibility between my reference genome and GTF file
rna-seq hisat2 alignment reference genome
5.6 years ago by Batu ▴ 250
8
votes
3
replies
862
views
How safe the UCSC is for patients data
RNA-Seq
updated 4.8 years ago by 82k • written 4.8 years ago by ▴ 260
8
votes
9
replies
1.5k
views
6 follow
Featurecount is 0 while TPM is 6289.54
TPM Count Feature
2.4 years ago by zhangmeng21 ▴ 10
8
votes
1
reply
1.6k
views
Genome Sequencing And Evolutionary History
evolution
updated 10.3 years ago by 49k • written 10.3 years ago by ▴ 110
8
votes
6
replies
981
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
6 months ago by Matteo Ungaro ▴ 100
8
votes
11
replies
2.7k
views
directionality of RRBS
directional non-directional RRBS
updated 2.8 years ago by ★ 2.9k • written 2.9 years ago by ▴ 140
8
votes
10
replies
845
views
bash script
whole-genome-sequencing
updated 5 weeks ago by 44k • written 6 weeks ago by ▴ 30
8
votes
6
replies
2.6k
views
for low coverage RNAseq how many reads assigned is the bare minimum for differential gene expression analysis
RNA-Seq
5.3 years ago by senowinski ▴ 30
8
votes
4
replies
2.4k
views
Global Sequence Alignment
alignment
11.0 years ago by behrang • 0
1,000 results • Page 5 of 20
Recent Votes
Comment: How to get the ratio of allele counts from GATK derived VCF file?
Setting up Aspera Connect (ascp) on Linux and macOS
Setting up Aspera Connect (ascp) on Linux and macOS
Answer: Genes' fpkm values through cufflink
Answer: Genes' fpkm values through cufflink
Genes' fpkm values through cufflink
Error when looping over multiple columns in a data frame in R
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Recent Replies
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by ATpoint 82k
Just for comparison, I deal with scRNA-seq daily and my workstation is a 12700k i7 with 128GB RAM and even this is actually more than I nee…
Answer: Ideal PC configurations and operating system for bioinformatics laboratory by colindaven 6.4k
- As others have said, 1-2 workstations are probably the way to go. - A Linux OS like Ubuntu is probably easiest and has best docs - RA…
Comment: How to get the ratio of allele counts from GATK derived VCF file? by anikcropscience ▴ 230
Ok, thank you for the reply. I will check out the DP field then.
Comment: Alternatives To Liftover by Thanujay S • 0
Hey! Would you consider building an API for the same? Is that something you have planned?
Answer: Ideal PC configurations and operating system for bioinformatics laboratory by emmanouil.a ▴ 120
20k are good money for some workstations ... probably you need to run more samples at the same time ... for some 1000s you could take a wor…
Comment: samtools write-index by LucisTheFather • 0
``` -o alignment.sorted.bam##idx##alignment.sorted.bam.bai ``` This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index by LucisTheFather • 0
Really appreciate your help Pierre! I am a little bit confused btw. do you mean this: ``` rm -vf alignment.sorted.bam.bai minimap2 -ax map-…
Comment: samtools write-index by LucisTheFather • 0
Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests) and none of…
Comment: Which 1000 genomes 30x files should I use for imputation? by David-walson • 0
Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
Comment: MAUVE: No gene annotations in Genbank file alignments by pramach1 ▴ 40
The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
Answer: Error when looping over multiple columns in a data frame in R by Jeremy ▴ 910
First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx by GenoMax 142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by GenoMax 142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by bk11 ★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files by a.penatauber • 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
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