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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
12
votes
21
replies
3.1k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
Miguel
▴ 30
0
votes
21
replies
948
views
Expression analysis of LncRNA from RNA-seq data
expression
lncrna
6 weeks ago by
analyst
▴ 10
4
votes
20
replies
1.8k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
4.2 years ago by
schlogl
▴ 160
5
votes
20
replies
4.0k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 18 months ago by
Ram
43k • written 8.6 years ago by
Hans
▴ 140
0
votes
20
replies
1.5k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
5 months ago by
langziv
▴ 50
8
votes
20
replies
2.4k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 22 months ago by
Ram
43k • written 5.7 years ago by
Bara'a
▴ 270
6
votes
20
replies
6.3k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.8 years ago by
princy149
▴ 80
5
votes
20
replies
8.2k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.6 years ago by
varsha619
▴ 90
9
votes
20
replies
4.1k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 12 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
22
votes
20
replies
2.5k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 11 months ago by
Ram
43k • written 7.7 years ago by
Farbod
★ 3.4k
8
votes
20
replies
2.9k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
6.2 years ago by
corend
▴ 70
2
votes
20
replies
2.2k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
6 months ago by
Maxine
▴ 40
8
votes
20
replies
2.5k
views
Getting read depth for normal and tumour
R
WGS
vcf
5.0 years ago by
zizigolu
★ 4.3k
6
votes
19
replies
2.8k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.7 years ago by
aloke205
▴ 40
22
votes
19
replies
3.1k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.5 years ago by
zizigolu
★ 4.3k
0
votes
19
replies
2.7k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.6 years ago by
rheab1230
▴ 140
9
votes
19
replies
2.3k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.2 years ago by
schlogl
▴ 160
7
votes
19
replies
2.9k
views
mapping script process sleeping on server.
alignment
updated 22 months ago by
Ram
43k • written 9.1 years ago by
lvogel
▴ 30
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.9 years ago by
Ram
43k • written 5.9 years ago by
Nadin.asal
• 0
10
votes
19
replies
3.3k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.9 years ago by
GenoMax
140k • written 2.9 years ago by
matt
▴ 20
0
votes
19
replies
1.9k
views
scatterplot in R
microarray
expression
gene
updated 18 months ago by
Ram
43k • written 18 months ago by
bioinformatics
▴ 40
3
votes
19
replies
1.4k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 8 months ago by
Asaf
10k • written 8 months ago by
captainlabman
▴ 20
0
votes
19
replies
3.8k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
6.2 years ago by
jaqx008
▴ 110
0
votes
19
replies
1.5k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
4.3 years ago by
marongiu.luigi
▴ 710
1
vote
19
replies
771
views
Matching transcriptomic data to clinical data
R
updated 7 weeks ago by
Ram
43k • written 7 weeks ago by
Khadija
▴ 10
5
votes
19
replies
3.9k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.8 years ago by
ta_awwad
▴ 340
0
votes
19
replies
9.4k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.8 years ago by
seta
★ 1.9k
1
vote
19
replies
2.0k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
5.3 years ago by
eozcan
▴ 10
1
vote
19
replies
6.9k
views
Conda install package - different internals
R
software error
updated 4.6 years ago by
Biostar
20 • written 4.6 years ago by
lihe.liu
▴ 30
5
votes
19
replies
1.7k
views
how I can come up with a permanent error
R
software error
6.9 years ago by
zizigolu
★ 4.3k
3
votes
19
replies
5.9k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.9 years ago by
finswimmer
16k • written 4.9 years ago by
sruthi
▴ 40
4
votes
19
replies
3.1k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.6 years ago by
Biostar
20 • written 6.7 years ago by
cool.abbecker
▴ 30
18
votes
19
replies
2.2k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 16 months ago by
Ram
43k • written 5.2 years ago by
rbkh09
• 0
17
votes
19
replies
2.7k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.6 years ago by
Gian77
▴ 60
13
votes
19
replies
5.3k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.3 years ago by
bioplanet
▴ 60
6
votes
19
replies
1.6k
views
Fastq header modification
sequence
next-gen
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Guillaume
• 0
7
votes
19
replies
7.0k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
mheiser1
▴ 10
0
votes
19
replies
1.3k
views
map fasts files
RNA-Seq
FASTQ
R
6.1 years ago by
Learner
▴ 280
2
votes
18
replies
6.1k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
7.4 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
2.3k
views
I need help in this
gene
weblems
alignment
updated 20 months ago by
Ram
43k • written 8.3 years ago by
efosa15
• 0
5
votes
18
replies
6.6k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
4.3 years ago by
michelle.piquet
▴ 60
1
vote
18
replies
1.7k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 4.6 years ago by
Biostar
20 • written 4.6 years ago by
Natasha
▴ 40
4
votes
18
replies
4.0k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 19 months ago by
Ram
43k • written 8.3 years ago by
Joel TM
▴ 60
7
votes
18
replies
4.8k
views
Fold change UP and Down in dplyr calculation
R
6.6 years ago by
1769mkc
★ 1.2k
4
votes
18
replies
2.9k
views
Inline barcodes in the reverse reads
barcodes
7.4 years ago by
Picasa
▴ 640
3
votes
18
replies
3.1k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.7 years ago by
Ram
43k • written 2.7 years ago by
Nai
▴ 50
1
vote
18
replies
2.7k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.7 years ago by
Tom
▴ 40
0
votes
18
replies
1.8k
views
freebayes error variant calling
snp
3.6 years ago by
evelyn
▴ 220
7
votes
18
replies
4.5k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
7.4 years ago by
valerie
▴ 100
0
votes
18
replies
1.7k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 7 months ago by
GenoMax
140k • written 7 months ago by
Apex92
▴ 280
1,000 results • Page
2 of 20
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Comment: Interproscan taking so much time
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Answer: Issue with making local BLAST database
Comment: struggle to get fasta files from ucsc goldenPath
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Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
• 0
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
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140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
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maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
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by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
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by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
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I downsampled the bams and it works now...
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You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
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