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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
0
votes
18
replies
1.5k
views
No gene name after annovar vcf file processing
vcf
annovar
4.5 years ago by
valerie
▴ 100
7
votes
18
replies
8.5k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
hana
▴ 190
2
votes
18
replies
2.6k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
2.2 years ago by
shivangi.agarwal800
▴ 120
4
votes
18
replies
16k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.4 years ago by
Biostar
20 • written 5.6 years ago by
Shelle
▴ 30
14
votes
18
replies
4.9k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.2 years ago by
Biostar
20 • written 7.4 years ago by
plink_9857
▴ 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
16
votes
18
replies
5.3k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.6 years ago by
Mensur Dlakic
★ 26k • written 4.6 years ago by
tikshyadav19
• 0
7
votes
18
replies
4.8k
views
Fold change UP and Down in dplyr calculation
R
6.6 years ago by
1769mkc
★ 1.2k
20
votes
17
replies
5.9k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.6 years ago by
Anand Rao
▴ 620
27
votes
17
replies
21k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.3 years ago by
Leite
★ 1.3k
2
votes
17
replies
4.3k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam
bam
alignment
samtools
updated 10.2 years ago by
Devon Ryan
104k • written 10.2 years ago by
Rohit
★ 1.5k
3
votes
17
replies
2.8k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing
faire
mapping
3.0 years ago by
boczniak767
▴ 850
5
votes
17
replies
4.2k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics
encode
10.1 years ago by
14134125465346445
★ 3.6k
1
vote
17
replies
2.3k
views
Normalizing BLAST results
blast
updated 6.5 years ago by
Biostar
20 • written 6.6 years ago by
db
• 0
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.6 years ago by
erincyurtman
• 0
1
vote
17
replies
5.7k
views
BBMap: Mapping Fails
BBTools
BBMap
Mapping
updated 8.0 years ago by
GenoMax
140k • written 8.0 years ago by
cacampbell
▴ 60
0
votes
17
replies
1.1k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
11 weeks ago by
Foad
▴ 10
7
votes
17
replies
3.8k
views
How to find the differences in aligned bam files
RNA-Seq
7.1 years ago by
1769mkc
★ 1.2k
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
3.5 years ago by
Dunois
★ 2.5k
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.4 years ago by
dimitrischat
▴ 210
0
votes
17
replies
2.7k
views
Fail running blastdb and blastn on my own computer
blast
6.4 years ago by
annette440
• 0
5
votes
17
replies
8.2k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.3 years ago by
C4
▴ 30
0
votes
17
replies
4.8k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 18 months ago by
Ram
43k • written 8.6 years ago by
jigarnt
▴ 30
20
votes
17
replies
3.1k
views
How to add "transcript" feature to a gtf file?
gtf
updated 8 months ago by
1769mkc
★ 1.2k • written 3.1 years ago by
pomodoro_sinensis
▴ 110
7
votes
17
replies
4.2k
views
Strange MA-plot using DESeq2
rna-seq
R
deseq2
updated 7.2 years ago by
Biostar
20 • written 7.3 years ago by
stan
▴ 80
8
votes
17
replies
3.9k
views
Getting nan value in vcftool relatedness command?
vcftools
relatedness
6.2 years ago by
Sharon
▴ 600
2
votes
17
replies
2.8k
views
Snakemake Megahit error
megahit
Snakemake
2.4 years ago by
blackadder
▴ 30
12
votes
17
replies
4.8k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.5 years ago by
anonymous1192976466
▴ 50
2
votes
17
replies
5.0k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 6.0 years ago by
h.mon
35k • written 6.0 years ago by
Janey
▴ 30
1
vote
17
replies
4.1k
views
Error executing bedops convert2bed
bedops
bed
vcf
convert2bed
7.2 years ago by
lakhujanivijay
5.8k
4
votes
17
replies
2.8k
views
Cufflinks analysis and gffread
RNA-Seq
Assembly
updated 6.4 years ago by
Kevin Blighe
87k • written 6.4 years ago by
qudrat
▴ 100
0
votes
17
replies
3.6k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq
wgcna
software error
R
next-gen
updated 2.2 years ago by
Dio
• 0 • written 5.5 years ago by
giuseppe0525
▴ 20
7
votes
17
replies
6.5k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R
gene
genome
5.7 years ago by
WUSCHEL
▴ 750
4
votes
17
replies
2.7k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray
gene-expression
CV
error
4.8 years ago by
Jurat Shahidin
▴ 100
2
votes
17
replies
9.4k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.1 years ago by
todd.ugine
• 0 • written 3.2 years ago by
merfer0206
• 0
3
votes
17
replies
1.5k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV
DownSample
fastq
copy number not accurate
4.1 years ago by
lffu_0032
▴ 90
6
votes
17
replies
2.3k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen
assembly
genome
alignment
5.8 years ago by
williamsbrian5064
▴ 510
0
votes
17
replies
3.0k
views
I am not able to let R read my file
R
fasta
updated 3.0 years ago by
Arup Ghosh
3.2k • written 3.0 years ago by
trejomarco6
• 0
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.8 years ago by
apl00028
▴ 90
0
votes
16
replies
4.5k
views
Issue using MaSuRCA-3.2.6
Assembly
assembler
updated 5.6 years ago by
Biostar
20 • written 5.8 years ago by
Chvatil
▴ 130
3
votes
16
replies
1.4k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 9 months ago by
Ram
43k • written 4.2 years ago by
Ankit
▴ 500
2
votes
16
replies
3.0k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.6 years ago by
Mostafa
▴ 20
7
votes
16
replies
2.7k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.2 years ago by
Chaimaa
▴ 260
9
votes
16
replies
1.8k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.4 years ago by
bioinfo456
▴ 150
15
votes
16
replies
1.6k
views
ncbi error report log for validate fastq issue
sra-tools
updated 6 months ago by
GenoMax
140k • written 6 months ago by
1769mkc
★ 1.2k
9
votes
16
replies
3.7k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 12 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
7
votes
16
replies
3.8k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing
genome-sequence
fastqc
genome
sequence
4.0 years ago by
Researcher
▴ 20
0
votes
16
replies
2.6k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 12 months ago by
Ram
43k • written 19 months ago by
yoser4
▴ 10
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools
sort
10.9 years ago by
chentong.biology
▴ 50
1,000 results • Page
3 of 20
Recent Votes
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
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