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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
2
votes
12
replies
985
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 10 weeks ago by
Ram
39k • written 11 weeks ago by
Human
• 0
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 7 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
12
replies
1.1k
views
Splitting CRAM files
CRAM-files
sequence-alignment
6 months ago by
langziv
▴ 30
1
vote
12
replies
1.2k
views
Volcano plot interpretation
EnhancedVolcano
volcano-plot
updated 3 months ago by
Ram
39k • written 23 months ago by
fahim
▴ 20
1
vote
12
replies
3.3k
views
dN/dS analysis of genomes
genome
sequence
alignment
7 months ago by
Mehmet
▴ 800
2
votes
12
replies
4.2k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 4 months ago by
Ram
39k • written 8.1 years ago by
cmogren
▴ 20
0
votes
12
replies
2.3k
views
Tax4Fun2 - error
tax4fun
silva
blast
updated 9 months ago by
GenoMax
130k • written 15 months ago by
ymj
▴ 10
1
vote
12
replies
3.2k
views
How to run multiple alignment and SNP-calling of WGS data in .gb and .fasta using Python or Ruby/Java or any free software?
alignment
sequencing
software
updated 11 months ago by
Ram
39k • written 8.2 years ago by
fashiondesignrussian
▴ 60
2
votes
12
replies
646
views
how to align an intron from a complex
genomic
updated 11 months ago by
WouterDeCoster
47k • written 11 months ago by
Bioinfo
• 0
8
votes
12
replies
2.7k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 11 weeks ago by
Ram
39k • written 22 months ago by
daver.v
▴ 30
4
votes
12
replies
1.1k
views
Bulk RNA seq: all p adjusted are the same
p-adj
RNA-seq
differential-gene-expression
updated 5 months ago by
Ram
39k • written 12 months ago by
nils.simon.biology
▴ 10
1
vote
12
replies
3.7k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 5 months ago by
ATpoint
73k • written 5.7 years ago by
SMILE
▴ 170
7
votes
12
replies
892
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 15 days ago by
Sasha
▴ 420 • written 21 days ago by
Chris
▴ 100
6
votes
12
replies
1.3k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 12 weeks ago by
Ram
39k • written 2.8 years ago by
akshaykum684
▴ 20
5
votes
12
replies
652
views
Data from an experiment
single-cell
updated 3 months ago by
GenoMax
130k • written 3 months ago by
Chris
▴ 100
0
votes
12
replies
1.6k
views
bedtools intersect issue
bed
bedtools
updated 11 weeks ago by
Ram
39k • written 4.8 years ago by
elisheva
▴ 120
2
votes
12
replies
1.8k
views
Nothing will align with HTSeq?
RNA-Seq
htseq
updated 8 months ago by
Ram
39k • written 7.7 years ago by
Kristin Muench
▴ 620
6
votes
12
replies
603
views
Help with error in cellranger
Cellranger
updated 23 days ago by
GenoMax
130k • written 24 days ago by
Chris
▴ 100
0
votes
12
replies
2.9k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 22 days ago by
Ram
39k • written 5.6 years ago by
fonteneaudam
▴ 20
6
votes
12
replies
1.2k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 11 weeks ago by
Ram
39k • written 4.4 years ago by
english.server
▴ 290
0
votes
12
replies
2.7k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen
Assembly
updated 5 months ago by
Ram
39k • written 7.9 years ago by
mafireyi
▴ 80
2
votes
12
replies
1.4k
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
8 months ago by
JACKY
▴ 100
4
votes
11
replies
6.6k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
9 months ago by
prasundutta87
▴ 650
6
votes
11
replies
932
views
Calculate RPKM
RPKM
11 weeks ago by
Chris
▴ 100
5
votes
11
replies
6.4k
views
Error while running miso
RNA-Seq
splicing
updated 10 months ago by
Ram
39k • written 7.8 years ago by
priyankamaripuri
▴ 40
4
votes
11
replies
1.1k
views
Running STAR
STAR
10 months ago by
Chris
▴ 100
1
vote
11
replies
3.1k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher
bedtools
intersection
updated 3 months ago by
Ram
39k • written 5.3 years ago by
jomo018
▴ 720
4
votes
11
replies
2.6k
views
7 follow
Getting coding sequence length
NCBI
Gene
CDS
updated 12 months ago by
newbio17
▴ 360 • written 2.9 years ago by
fi1d18
★ 4.2k
0
votes
11
replies
892
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 4 months ago by
GenoMax
130k • written 4 months ago by
john
• 0
8
votes
11
replies
1.4k
views
using STAR instead of HISAT2
STAR
updated 10 months ago by
Ram
39k • written 10 months ago by
Chris
▴ 100
0
votes
11
replies
1.5k
views
Error in Importing data in qiime2
Metagenomics
Sequencing
Qiime2
Amplicon
11 months ago by
Vaishnavi
• 0
5
votes
11
replies
3.1k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 12 weeks ago by
Ram
39k • written 5.1 years ago by
HG
▴ 30
4
votes
11
replies
2.7k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 4 months ago by
Ram
39k • written 5.1 years ago by
mahdikhadem95
▴ 30
0
votes
11
replies
936
views
Python - Samtools mpileup find snps with allele frequency
snp
mpileup
python
samtools
11 months ago by
pablosolar.r
▴ 20
1
vote
11
replies
3.0k
views
merge samples in phyloseq returns NAs
R
phyloseq
biom
updated 7 months ago by
joe.e.weaver
• 0 • written 2.9 years ago by
annaA
▴ 10
3
votes
11
replies
895
views
RepeatMasker error
repeatmasking
transciptome
RNA-seq
updated 11 months ago by
mark.ziemann
★ 1.8k • written 11 months ago by
barrypraveen
▴ 110
1
vote
10
replies
2.4k
views
Issue in running viroBlast from localhost
blast
php
viroBlast
javascript
sequence
updated 11 months ago by
Ram
39k • written 7.3 years ago by
arfaj a
▴ 10
3
votes
10
replies
997
views
Error with FindConservedMarkers()
FindConservedMarkers
3 months ago by
Chris
▴ 100
4
votes
10
replies
3.7k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 4 months ago by
Ram
39k • written 8.1 years ago by
David_emir
▴ 460
5
votes
10
replies
4.7k
views
Antisense transcription - how to detect it?
RNA-Seq
antisense
updated 9 months ago by
Ram
39k • written 7.7 years ago by
John
13k
0
votes
10
replies
2.3k
views
eXpress error gene length different
eXpress
rna-seq
updated 11 months ago by
Ram
39k • written 8.1 years ago by
bharata1803
▴ 550
2
votes
10
replies
3.2k
views
concatenate multiple GZip fastq files from multilane run and output combined gzip file
perl
fastqc
next-gen-sequencing
updated 10 months ago by
Ram
39k • written 7.5 years ago by
PAn
▴ 20
4
votes
10
replies
452
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
3 months ago by
dps2501
▴ 20
1
vote
10
replies
2.6k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 13 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
5
votes
10
replies
435
views
Error when viewing a bam file
samtools
5 weeks ago by
Chris
▴ 100
0
votes
10
replies
2.0k
views
WGCNA, module trait relationship
R
updated 8 months ago by
priya.bmg
▴ 60 • written 2.8 years ago by
sadeghi.reyhane
• 0
5
votes
10
replies
936
views
How to change chromosome names in assembly fasta downloaded from NCBI?
grch38
ncbi
grch37
fasta
8 months ago by
magnolia
▴ 20
0
votes
10
replies
3.1k
views
6 follow
Error message running GeMoMa
gene
updated 9 months ago by
GenoMax
130k • written 3.9 years ago by
valopes
▴ 30
6
votes
10
replies
896
views
Understanding bam tracks
RNA
sequencing
bam
updated 9 months ago by
Pierre Lindenbaum
155k • written 9 months ago by
Tonkatsu
▴ 30
0
votes
10
replies
1.3k
views
DeSeq2 "some values in assay are negative"
RNAseq
7 months ago by
Morris_Chair
▴ 330
1,000 results • Page
2 of 20
Recent Votes
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
Answer: Extract variants/SNPs with T>G substitution from a VCF file
PRSice-2 using SNPs with extremely low P-value
Answer: PRSice-2 using SNPs with extremely low P-value
Filtering content in heatmap to highest values
conda: command not found: gatk.
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Recent Replies
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
That's an excellent point. A significant number of students are engaged in academic misconduct due to the use of fabricated references and …
Comment: Filtering content in heatmap to highest values
by
Papyrus
★ 2.5k
You mean something like this? depends on how you define "top" row or column # Create example (it is a data.table) ListerTFHeat <- …
Comment: conda: command not found: gatk.
by
666billgaytes
• 0
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file
by
4galaxy77
2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow
by
Dr William Klubinski
▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity
by
Ben_Ensembl
★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Comment: conda: command not found: gatk.
by
bestone
▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk.
by
bestone
▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
155k
> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk.
by
bestone
▴ 20
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
155k
how about all your previous questions ? take a time to validate the good answers (green mark on the left). https://www.biostars.org/p/9565…
Answer: No @hd header returned in sam file when running bwa mem
by
Pierre Lindenbaum
155k
the HD header is not generated by bwa, but you can add it using awk: bwa (...) | awk '(NR==1) {printf("@HD\tVN:1.6\tSO:unknown\n");}{…
Comment: Ensembl vep singularity
by
Kiran
▴ 80
Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?
Answer: No @hd header returned in sam file when running bwa mem
by
GokalpC
▴ 80
Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort. ANGSD…
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