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389 results • Page
1 of 8
Sort: Votes
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Votes
Replies
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 5 days ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 4 days ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 4 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 4 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 5 days ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 4 days ago by
Ram
38k • written 16 months ago by
Nikhil
▴ 10
6
votes
11
replies
737
views
Calculate RPKM
RPKM
6 days ago by
Chris
▴ 70
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 6 days ago by
Ram
38k • written 8.0 years ago by
gaurav.singh
▴ 10
5
votes
6
replies
2.9k
views
Changes log2FC values of DESeq2
log2FC
DESeq2
updated 3 days ago by
Ram
38k • written 5.3 years ago by
realnewbie
▴ 30
5
votes
4
replies
1.7k
views
MyVariant.info fields descriptions?
genome
snp
variant
updated 3 days ago by
Ram
38k • written 6.9 years ago by
Nolwenn Lavielle
▴ 90
4
votes
3
replies
189
views
Geom bar postive and negative values in a flipped plot
flip_coord
ggplot
geom_bar
3 days ago by
luzglongoria
▴ 40
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf
bcftools
updated 4 days ago by
Ram
38k • written 3.2 years ago by
Begonia_pavonina
▴ 90
4
votes
2
replies
906
views
Convert BAM files to GENOMEDATA files
BAM
genomedata
updated 4 days ago by
Ram
38k • written 4.9 years ago by
Armand
• 0
4
votes
7
replies
2.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 4 days ago by
Ram
38k • written 21 months ago by
mathavanbioinfo
▴ 70
3
votes
4
replies
262
views
Creating sample groups from a combination of genes for survival analysis
Survival
4 days ago by
krushnach80
★ 1.1k
3
votes
4
replies
482
views
Changing Temporary File Location for Local BLASTP to nr Database
protein
blast
nr
updated 6 days ago by
Ram
38k • written 10 weeks ago by
katieostrouchov
▴ 20
3
votes
2
replies
244
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
PAAD
KM
Plot
TCGA
4 days ago by
Manav
• 0
3
votes
2
replies
160
views
Power analysis for patient samples
RNA-seq
5 days ago by
aropri
▴ 130
3
votes
2
replies
210
views
correlations in R
cor
R
4 days ago by
rene.j.erhardt
▴ 20
3
votes
4
replies
330
views
How much reads per cell for fusion detection with Nanopore ?
single-cell
fusion
nanopore
3 days ago by
Evan
▴ 180
3
votes
2
replies
506
views
[bam-readcount v.0.8.0] Fail to open BAM file –q
bam-readcount
BAM
updated 4 days ago by
Ram
38k • written 22 months ago by
vanessagpds
▴ 10
3
votes
4
replies
1.4k
views
How to get regions with mapped reads
bed
bam
RNA-Seq
bedtools
updated 4 days ago by
Ram
38k • written 4.5 years ago by
nanoide
▴ 100
3
votes
4
replies
1.5k
views
Which files from PacBio output files to use in downstream analysis in R
R
PacBio
updated 4 days ago by
Ram
38k • written 18 months ago by
eimanpharmacist
▴ 20
3
votes
8
replies
290
views
getting coding exon information from Ensembl API
Ensembl
API
updated 4 days ago by
Ram
38k • written 4 days ago by
Nobody
▴ 30
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure
splign
updated 5 days ago by
Ram
38k • written 6.4 years ago by
Esaie
▴ 160
3
votes
3
replies
336
views
Retrieving information from FASTA file
NGS
FASTA
VCF
updated 5 days ago by
Ram
38k • written 12 months ago by
Maryam
▴ 10
3
votes
0
replies
1.8k
views
Combined VCF file for all GTEx genotype calls?
GTExv7
GTEx
Genotype
dbGap
VCF
updated 4 days ago by
Ram
38k • written 5.5 years ago by
django.waddle
▴ 60
2
votes
3
replies
210
views
RNAseq: same reads + more complete scaffold = fewer DEGs?
RNAseq
updated 3 days ago by
Darked89
4.2k • written 4 days ago by
phillip.brassington
▴ 10
2
votes
1
reply
1.1k
views
pacbio db and las files
db
pacbio
las
next-gen
updated 4 days ago by
Ram
38k • written 5.8 years ago by
biomagician
▴ 350
2
votes
7
replies
775
views
Import data for igraph using R
r
igraph
updated 5 days ago by
Ram
38k • written 12 months ago by
kaisakaiho73847
• 0
2
votes
2
replies
456
views
Unable to read fasta file
fasta
updated 4 days ago by
Ram
38k • written 21 months ago by
Aritra
• 0
2
votes
12
replies
523
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 2 days ago by
Ram
38k • written 4 days ago by
Human
• 0
2
votes
3
replies
507
views
BWA generating a sam file without alignment information
sam
bwa
updated 5 days ago by
Ram
38k • written 13 months ago by
kelsey.e.witt
• 0
2
votes
6
replies
1.0k
views
GFF3 TO GTF CONVERSION
GFF3
Hydra
GFF
GTF
updated 5 days ago by
Ram
38k • written 14 months ago by
Shagnik
• 0
2
votes
4
replies
240
views
Error with a function in ATAC-seq analysis
ATAC-seq
3 days ago by
Chris
▴ 70
2
votes
2
replies
1.3k
views
Perl script problem: Remove duplicates from my fasta file with help of perl
perl
Fasta
updated 4 days ago by
Ram
38k • written 5.0 years ago by
ArusjakGevorgyan
▴ 20
2
votes
0
replies
489
views
3D distance between two chromosomal coordinates in 3D human genome?
3d
hi-C
genome
chia-pet
updated 3 days ago by
Ram
38k • written 2.0 years ago by
robert.mclaughlin
▴ 20
2
votes
5
replies
559
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 5 days ago by
igor
13k • written 9 days ago by
e.r.zakiev
▴ 30
2
votes
9
replies
1.9k
views
SAM file quality check without converting into BAM
Alignment
SAM
updated 4 days ago by
Ram
38k • written 3.8 years ago by
vaish01kv
• 0
2
votes
2
replies
3.0k
views
R:how to read bed file with identical Famliy ID by read.plink
bed
plink
R
updated 4 days ago by
Ram
38k • written 6.7 years ago by
zwang10
▴ 30
2
votes
1
reply
211
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 5 days ago by
Basti
★ 1.4k • written 6 days ago by
Stefanus C.B.
• 0
2
votes
6
replies
312
views
bioinformatics problems solved by graphs data structure
Graph
algorithm
data-structure
updated 3 days ago by
Ram
38k • written 3 days ago by
abdelmalek.benmeziane
• 0
2
votes
3
replies
419
views
Genomics regions that common to atleast 10 cell types
bedtools
bedops
genome
bed
sequence
updated 3 days ago by
Ram
38k • written 2.8 years ago by
rohitsatyam102
▴ 690
2
votes
3
replies
343
views
HaplotypeCaller GENOTYPE GIVEN ALLELES doesn't genotype given alleles
Gatk
HaplotypeCaller
VCF
updated 4 days ago by
dthorbur
▴ 420 • written 4 weeks ago by
kamanovae
▴ 80
1
vote
2
replies
931
views
Downloading 1000genome phase 3 data in 38 build
1000genomes
updated 3 days ago by
Ram
38k • written 2.1 years ago by
AVA
▴ 40
1
vote
2
replies
215
views
Weird looking dispersion & MA plot?
deseq2
RNA-seq
updated 3 days ago by
Ram
38k • written 4 days ago by
Neha
• 0
1
vote
2
replies
1.9k
views
How can find LD between rows (SNPs) two by two?
linkage-Disequilibrium
genomics
R
updated 5 days ago by
Ram
38k • written 7.1 years ago by
star
▴ 330
1
vote
1
reply
460
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 5 days ago by
Ram
38k • written 11 months ago by
ManuelDB
▴ 30
1
vote
3
replies
692
views
Problem when downloading Fastq files from ENA Database automatically with accession number
ENA
Fastq
updated 3 days ago by
Ram
38k • written 17 months ago by
ignacio.martinezdelejarza
• 0
1
vote
7
replies
857
views
Splitting BED file by technical replicate or extract all unique barcodes
BED
updated 4 days ago by
Ram
38k • written 2.7 years ago by
summer_researcher
• 0
389 results • Page
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Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Answer: getTable ignores query ranges
by
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• 0
The short answer is you can theoretically do this you just need to a) make your SNPs are two base-pairs in length (i.e. add 1 to the end) a…
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Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
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I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
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Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
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Perfect answer, thanks Ben!
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Any updates??
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Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
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If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq
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@ATpoint, so no adapter trimming first? Just trim the raw fastq?
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Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
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127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq
by
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127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
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70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
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I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
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70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
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