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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
7
votes
21
replies
3.1k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.5 years ago by
jmsyl.hong
• 0
16
votes
21
replies
2.2k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.6 years ago by
Farbod
★ 3.4k
9
votes
20
replies
4.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 13 months ago by
Ram
43k • written 5.7 years ago by
marongiu.luigi
▴ 710
5
votes
20
replies
8.3k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.7 years ago by
varsha619
▴ 90
8
votes
20
replies
2.6k
views
Getting read depth for normal and tumour
R
WGS
vcf
5.1 years ago by
zizigolu
★ 4.3k
6
votes
20
replies
6.4k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.9 years ago by
princy149
▴ 80
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
6 months ago by
langziv
▴ 50
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 12 months ago by
Ram
43k • written 7.8 years ago by
Farbod
★ 3.4k
8
votes
20
replies
2.9k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
6.3 years ago by
corend
▴ 70
5
votes
20
replies
4.1k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Hans
▴ 140
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 23 months ago by
Ram
43k • written 5.7 years ago by
Bara'a
▴ 270
4
votes
20
replies
1.9k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
4.3 years ago by
schlogl
▴ 160
2
votes
20
replies
2.3k
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
7 months ago by
Maxine
▴ 40
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
3
votes
19
replies
1.5k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 9 months ago by
Asaf
10k • written 9 months ago by
captainlabman
▴ 20
9
votes
19
replies
2.3k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by
schlogl
▴ 160
6
votes
19
replies
1.7k
views
Fastq header modification
sequence
next-gen
updated 6.1 years ago by
Ram
43k • written 6.1 years ago by
Guillaume
• 0
1
vote
19
replies
2.1k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
5.4 years ago by
eozcan
▴ 10
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
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Nadin.asal
• 0
18
votes
19
replies
2.3k
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 5.3 years ago by
rbkh09
• 0
0
votes
19
replies
3.8k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
6.3 years ago by
jaqx008
▴ 110
0
votes
19
replies
9.5k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.9 years ago by
seta
★ 1.9k
13
votes
19
replies
5.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.4 years ago by
bioplanet
▴ 60
17
votes
19
replies
2.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.6 years ago by
Gian77
▴ 60
1
vote
19
replies
856
views
Matching transcriptomic data to clinical data
R
updated 11 weeks ago by
Ram
43k • written 11 weeks ago by
Khadija
▴ 10
10
votes
19
replies
3.4k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.9 years ago by
GenoMax
141k • written 2.9 years ago by
matt
▴ 20
7
votes
19
replies
2.9k
views
mapping script process sleeping on server.
alignment
updated 23 months ago by
Ram
43k • written 9.1 years ago by
lvogel
▴ 30
5
votes
19
replies
1.7k
views
how I can come up with a permanent error
R
software error
7.0 years ago by
zizigolu
★ 4.3k
5
votes
19
replies
4.0k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.9 years ago by
ta_awwad
▴ 340
0
votes
19
replies
1.5k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
4.4 years ago by
marongiu.luigi
▴ 710
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 9.5 years ago by
mheiser1
▴ 10
0
votes
19
replies
1.4k
views
map fasts files
RNA-Seq
FASTQ
R
6.2 years ago by
Learner
▴ 280
0
votes
19
replies
2.8k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.7 years ago by
rheab1230
▴ 140
1
vote
19
replies
7.0k
views
Conda install package - different internals
R
software error
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
lihe.liu
▴ 30
3
votes
19
replies
6.0k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 5.0 years ago by
finswimmer
16k • written 5.0 years ago by
sruthi
▴ 40
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.5 years ago by
zizigolu
★ 4.3k
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 6.8 years ago by
cool.abbecker
▴ 30
2
votes
18
replies
6.2k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
7.4 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
2.4k
views
I need help in this
gene
weblems
alignment
updated 20 months ago by
Ram
43k • written 8.3 years ago by
efosa15
• 0
3
votes
18
replies
1.9k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
18 months ago by
lacb
▴ 120
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
4
votes
18
replies
4.1k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Joel TM
▴ 60
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 8 months ago by
GenoMax
141k • written 8 months ago by
Apex92
▴ 280
0
votes
18
replies
1.6k
views
No gene name after annovar vcf file processing
vcf
annovar
4.5 years ago by
valerie
▴ 100
2
votes
18
replies
2.7k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
2.3 years ago by
shivangi.agarwal800
▴ 120
4
votes
18
replies
3.0k
views
Inline barcodes in the reverse reads
barcodes
7.5 years ago by
Picasa
▴ 640
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 4.7 years ago by
Natasha
▴ 40
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
21 days ago by
b.contreras.moreira
▴ 170
7
votes
18
replies
4.6k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
7.5 years ago by
valerie
▴ 100
1,000 results • Page
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Recent Votes
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
Pierre Lindenbaum
161k
see also : https://www.biostars.org/p/9537698/ ; https://www.biostars.org/p/9464312/ ; https://www.biostars.org/p/417123/
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
Pierre Lindenbaum
161k
what's the gray section ? it's the read you want ? do you only want the reads that end at the splice event (single point location) ?
Comment: interpretartion of a vcf file
by
Pierre Lindenbaum
161k
yes if there is more than one sample genotyped.
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
Is it typical to observe such a profile in the context of diploid organism ?
Answer: Plots for DNA methylation data
by
Basti
★ 2.0k
Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a…
Comment: Heatmap and rna-seq
by
Basti
★ 2.0k
This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
Answer: python file for coding potential calculator
by
atharvakarkare14
▴ 10
Download the CPC2 tool supported by python 3 from here [https://github.com/gao-lab/CPC2_standalone/releases/tag/v1.0.1][1]. Then follow …
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
More than likely not since the database query seems to work for the redirected PMID but not the original. $ esearch -db pubmed -query …
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
Blast showed PDB: 8J07_n9(human) as best template with 62.99%. I also used swissmodel to model the protein and it showed: https://swissmod…
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
No, in haplotypecaller
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
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