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785 results • Page
1 of 16
Sort: Views
Rank
Views
Votes
Replies
124
votes
13
replies
165k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 21 days ago by
Ram
40k • written 13.2 years ago by
Biomed
4.9k
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 4 days ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 7 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
146
votes
70
replies
46k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 29 days ago by
Raheleh
▴ 260 • written 5.8 years ago by
Kevin Blighe
86k
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 8 days ago by
zx8754
11k • written 10.7 years ago by
henryvuong
▴ 810
81
votes
21
replies
40k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 12 days ago by
Joel Wallenius
▴ 180 • written 9.6 years ago by
pristanna
▴ 750
19
votes
10
replies
29k
views
6 follow
read depth using samtools
depth
samtools
updated 12 days ago by
Sachin
• 0 • written 4.7 years ago by
LimMo
▴ 30
100
votes
38
replies
29k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 27 days ago by
Jeremy Leipzig
21k • written 9.9 years ago by
14134125465346445
★ 3.6k
36
votes
16
replies
28k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 7 days ago by
jkbonfield
★ 1.1k • written 4.6 years ago by
chparada
▴ 60
298
votes
122
replies
28k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 22 days ago by
jena
▴ 270 • written 13.2 years ago by
Eric Normandeau
11k
36
votes
23
replies
27k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 25 days ago by
s.w.vanderlaan
▴ 40 • written 2.2 years ago by
Michal Nevo
▴ 110
10
votes
5
replies
25k
views
FastQC with multiple FASTQ files
ngs
fastqc
multiple
updated 8 days ago by
Ram
40k • written 5.3 years ago by
m98
▴ 400
21
votes
9
replies
21k
views
9 follow
Building Snpeff Database
vcftools
snp
gatk
updated 21 days ago by
Ram
40k • written 11.1 years ago by
bioinfo
▴ 830
33
votes
23
replies
18k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 13 days ago by
alejandrogzi
▴ 30 • written 5.5 years ago by
JJ
▴ 660
31
votes
9
replies
17k
views
6 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 12 hours ago by
Ram
40k • written 7.1 years ago by
bioinformatics.cancer
▴ 240
18
votes
10
replies
14k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene
RNA-Seq
next-gen
fold-change
updated 11 days ago by
Ram
40k • written 3.9 years ago by
WUSCHEL
▴ 720
12
votes
5
replies
13k
views
How to combine chromosome vcf files
Assembly
alignment
next-gen
genome
updated 25 days ago by
Pierre Lindenbaum
157k • written 5.3 years ago by
williamsbrian5064
▴ 480
10
votes
13
replies
12k
views
6 follow
How to annotate only selected genes on a heatmap
R
updated 22 days ago by
GenoMax
134k • written 6.3 years ago by
h.fushimi.x689
▴ 30
10
votes
8
replies
11k
views
8 follow
How to install gdc-client in Ubnutu
ubuntu
gdc-client
updated 15 days ago by
Ram
40k • written 7.1 years ago by
pxf109
▴ 20
3
votes
6
replies
11k
views
Retrieving data from NCBI GEO and RNA-Seq Data Analysis
RNA-Seq
R
GEO
Normalization
Count
updated 1 day ago by
Karma
▴ 310 • written 6.1 years ago by
hkarakurt
▴ 170
7
votes
6
replies
10k
views
7 follow
Blastn Segmentation Fault
blast
updated 21 days ago by
Amirhossein Hajianpour
▴ 40 • written 11.8 years ago by
Srihari
▴ 30
4
votes
4
replies
8.7k
views
MaxEntScan score interpretation
splice-scores
MaxEntScan
updated 16 days ago by
Akshita
• 0 • written 4.7 years ago by
ga87mit
▴ 20
38
votes
25
replies
8.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 14 days ago by
Ram
40k • written 7.5 years ago by
waqasnayab
▴ 250
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 4 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
1
vote
1
reply
7.1k
views
Docker error "Mounts denied" running example workflows from CWL User Guide on Mac OS X
OSX
cwl
docker
macOS
Common-Workflow-Language
updated 15 days ago by
Ram
40k • written 6.3 years ago by
Kevin Ernst
• 0
9
votes
5
replies
7.0k
views
Genomic Bam To Transcriptome Bam
bam
samtools
updated 7 days ago by
Ram
40k • written 9.8 years ago by
dfernan
▴ 750
9
votes
7
replies
6.7k
views
Gc Content From Bam
gc
bam
awk
perl
updated 25 days ago by
Ram
40k • written 9.6 years ago by
filipzembol
▴ 170
13
votes
13
replies
6.5k
views
6 follow
Extract SNPs flanking sequences based on VCF and genome Fasta files
snp
sequence
genome
updated 28 days ago by
LauGuillardin
• 0 • written 5.1 years ago by
Denis
▴ 280
36
votes
5
replies
5.8k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 18 days ago by
gallardodiazmiriam
▴ 20 • written 8.2 years ago by
Luke Crichton
▴ 410
1
vote
4
replies
5.7k
views
How to order a gff3 file by coordinates
gff3
ordering
updated 14 days ago by
alejandrogzi
▴ 30 • written 5.6 years ago by
Antonio R. Franco
★ 5.1k
2
votes
7
replies
5.5k
views
Specific gene labeling in a heatmap
RNA-Seq
updated 22 days ago by
GenoMax
134k • written 3.2 years ago by
clizama
• 0
1
vote
8
replies
5.5k
views
"bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out how to fix my script
software-error
alignment
Assembly
bowtie2
written 4.6 years ago by
meerapprasad
▴ 10
6
votes
6
replies
5.3k
views
How is logFC and p-value estimated (for volcano plots)?
R
edgeR
fold-Change
updated 11 days ago by
Ram
40k • written 6.5 years ago by
LRStar
▴ 200
5
votes
8
replies
5.3k
views
6 follow
How to repair corrupted fastq files after sortmeRNA
software error
RNA-Seq
alignment
updated 9 days ago by
Tommaso
• 0 • written 5.6 years ago by
SMILE
▴ 170
0
votes
4
replies
5.3k
views
PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset
tcga
RNA-Seq
gdc
ebplusplus
updated 18 days ago by
bstrs
• 0 • written 4.6 years ago by
Ld_60
▴ 50
4
votes
8
replies
5.3k
views
Convert bed12 to GFF
bed
gff
bed12
updated 25 days ago by
Juke34
8.2k • written 6.6 years ago by
cmdcolin
★ 3.2k
9
votes
8
replies
5.2k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen
cnv
software-error
sequencing
updated 24 days ago by
Avinash
• 0 • written 9.3 years ago by
Kizuna
▴ 860
1
vote
1
reply
4.4k
views
Create writable directory inside container before executing baseCommand. How to properly use InitialWorkDirRequirement
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 7.0 years ago by
misha.kotliar
▴ 10
2
votes
10
replies
4.4k
views
CWL: Getting the outputs(File) of a command line tool
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 6.4 years ago by
kevin.o.oluoch
▴ 70
9
votes
5
replies
4.2k
views
CWL: how to set default values
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 6.9 years ago by
bird77
▴ 80
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 6 days ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
2
votes
7
replies
4.0k
views
GERP++ (gerpcol) error on a test data
GERP
updated 5 days ago by
Diana
• 0 • written 7.1 years ago by
kirill1984
▴ 10
8
votes
7
replies
4.0k
views
Problem in indexing toplevel genome with HISAT2
RNA-Seq
genome
hisat2
hisat2-build
index
updated 27 days ago by
Apex92
▴ 270 • written 4.6 years ago by
Batu
▴ 240
7
votes
7
replies
3.8k
views
Genes with promoter and enhancer regions as GTF
ChIP-Seq
featurecounts
gtf
promoter
genes
updated 3 days ago by
abis.1819104
• 0 • written 5.3 years ago by
hkarakurt
▴ 170
8
votes
10
replies
3.6k
views
Dataset's name in BioMart for S. pombe
S.pombe
BioMart
dataset
updated 1 hour ago by
YUYANG.OON
• 0 • written 9.3 years ago by
Parham
★ 1.6k
2
votes
2
replies
3.6k
views
Insert size is so small, good or bad?
Insert-size
RNA-Seq
updated 20 days ago by
Ram
40k • written 5.9 years ago by
Tania
▴ 180
9
votes
8
replies
3.5k
views
bcftools multiallelic split not working
bcftools
vcf
updated 12 hours ago by
Ram
40k • written 2.1 years ago by
from the mountains
▴ 220
4
votes
12
replies
3.4k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 14 days ago by
alejandrogzi
▴ 30 • written 3.4 years ago by
William
★ 5.2k
11
votes
7
replies
3.4k
views
7 follow
Assembler for only nanopore data
genomics
Assembly
ONT
Abyss
updated 15 days ago by
GenoMax
134k • written 4.4 years ago by
ringourquia
▴ 20
7
votes
15
replies
3.3k
views
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index
next-gen
sequencing
updated 7 days ago by
Gabriel R.
★ 2.9k • written 3.3 years ago by
Rezenman
• 0
785 results • Page
1 of 16
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Answer: Fetch Fastq files directly for SRA data
by
Rob
6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
by
YUYANG.OON
• 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
by
Chris
▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject
by
Qi
• 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis?
by
Yogi
▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions
by
Yogi
▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate
by
dsull
★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian)
by
morovatunc
▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes?
by
Michael
53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate
by
Mehwish
• 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting
by
Ram
40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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