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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
20
replies
1.3k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.4 years ago by
schlogl
▴ 150
9
votes
20
replies
3.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 10 weeks ago by
Ram
39k • written 4.8 years ago by
marongiu.luigi
▴ 680
6
votes
20
replies
5.6k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.0 years ago by
princy149
▴ 80
8
votes
20
replies
2.3k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.4 years ago by
corend
▴ 70
8
votes
20
replies
1.8k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.2 years ago by
fi1d18
★ 4.2k
5
votes
20
replies
3.3k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 8 months ago by
Ram
39k • written 7.8 years ago by
Hans
▴ 130
5
votes
20
replies
7.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
6.8 years ago by
varsha619
▴ 90
8
votes
20
replies
1.9k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 12 months ago by
Ram
39k • written 4.9 years ago by
Bara'a
▴ 270
6
votes
19
replies
2.3k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
3.9 years ago by
aloke205
▴ 40
0
votes
19
replies
1.1k
views
map fasts files
RNA-Seq
FASTQ
R
5.3 years ago by
Learner
▴ 260
4
votes
19
replies
2.5k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
cool.abbecker
▴ 30
0
votes
19
replies
1.1k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
3.5 years ago by
marongiu.luigi
▴ 680
7
votes
19
replies
6.4k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 16 months ago by
Ram
39k • written 8.6 years ago by
mheiser1
▴ 10
1
vote
19
replies
5.9k
views
Conda install package - different internals
R
software error
updated 3.8 years ago by
Biostar
20 • written 3.8 years ago by
lihe.liu
▴ 30
0
votes
19
replies
8.3k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.0 years ago by
seta
★ 1.8k
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.8 years ago by
Gian77
▴ 60
0
votes
19
replies
3.3k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.4 years ago by
jaqx008
▴ 110
18
votes
19
replies
1.7k
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 6 months ago by
Ram
39k • written 4.4 years ago by
rbkh09
• 0
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by
Ram
39k • written 5.1 years ago by
Nadin.asal
• 0
3
votes
19
replies
4.9k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.1 years ago by
finswimmer
16k • written 4.1 years ago by
sruthi
▴ 40
22
votes
19
replies
2.5k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.7 years ago by
fi1d18
★ 4.2k
5
votes
19
replies
1.3k
views
how I can come up with a permanent error
R
software error
6.1 years ago by
fi1d18
★ 4.2k
6
votes
19
replies
1.3k
views
Fastq header modification
sequence
next-gen
updated 5.2 years ago by
Ram
39k • written 5.2 years ago by
Guillaume
• 0
7
votes
19
replies
2.4k
views
mapping script process sleeping on server.
alignment
updated 13 months ago by
Ram
39k • written 8.3 years ago by
lvogel
▴ 30
0
votes
19
replies
1.2k
views
scatterplot in R
microarray
expression
gene
updated 8 months ago by
Ram
39k • written 8 months ago by
bioinformatics
▴ 10
9
votes
19
replies
1.7k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.4 years ago by
schlogl
▴ 150
0
votes
19
replies
2.2k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
22 months ago by
rheab1230
▴ 140
1
vote
19
replies
1.6k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
4.5 years ago by
eozcan
▴ 10
13
votes
19
replies
4.5k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.5 years ago by
bioplanet
▴ 60
10
votes
19
replies
2.6k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.1 years ago by
GenoMax
129k • written 2.1 years ago by
matt
▴ 20
2
votes
18
replies
5.3k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
6.6 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
1.8k
views
I need help in this
gene
weblems
alignment
updated 10 months ago by
Ram
39k • written 7.4 years ago by
efosa15
• 0
16
votes
18
replies
4.2k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.8 years ago by
Mensur Dlakic
★ 23k • written 3.8 years ago by
tikshyadav19
• 0
3
votes
18
replies
2.1k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 23 months ago by
Ram
39k • written 23 months ago by
Nai
▴ 50
7
votes
18
replies
4.1k
views
Fold change UP and Down in dplyr calculation
R
5.8 years ago by
1769mkc
★ 1.1k
2
votes
18
replies
1.9k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
17 months ago by
shivangi.agarwal800
▴ 120
4
votes
18
replies
3.4k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 10 months ago by
Ram
39k • written 7.5 years ago by
Joel TM
▴ 60
14
votes
18
replies
4.2k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
plink_9857
▴ 50
5
votes
18
replies
5.3k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
3.5 years ago by
michelle.piquet
▴ 60
4
votes
18
replies
2.6k
views
Inline barcodes in the reverse reads
barcodes
6.6 years ago by
Picasa
▴ 640
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.6 years ago by
Biostar
20 • written 4.8 years ago by
Shelle
▴ 30
3
votes
18
replies
1.1k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
7 months ago by
lacb
▴ 120
7
votes
18
replies
4.0k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
6.6 years ago by
valerie
▴ 100
1
vote
18
replies
1.2k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 3.8 years ago by
Biostar
20 • written 3.8 years ago by
Natasha
▴ 40
0
votes
18
replies
1.0k
views
No gene name after annovar vcf file processing
vcf
annovar
3.6 years ago by
valerie
▴ 100
1
vote
18
replies
2.2k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
6.8 years ago by
Tom
▴ 40
0
votes
18
replies
1.3k
views
freebayes error variant calling
snp
2.8 years ago by
evelyn
▴ 220
7
votes
18
replies
7.7k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 16 months ago by
Ram
39k • written 8.6 years ago by
hana
▴ 190
20
votes
17
replies
5.2k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.8 years ago by
Anand Rao
▴ 560
0
votes
17
replies
1.1k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
2.7 years ago by
Dunois
★ 2.3k
1,000 results • Page
2 of 20
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. The `counts` is log2-normalized raw data.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Ayish
• 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix?
by
Thu
• 0
Hi! Thanks for sharing your solution! It works! :)
Comment: Gene prediction software
by
Darked89
4.4k
Looks like there are five Clarias genomes: * https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp] The most complete seems t…
Comment: Alignment of case vs. control from different origin
by
sativus
▴ 10
Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
Answer: Extract sequences from a fastq file by a list of IDs
by
colindaven
4.9k
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
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