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Limit : this year
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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
3
votes
12
replies
874
views
why 99% reads failed to align in mir-seq analysis?
Fastqc
bowtie1
miRNA-seq
alignment
differential-expression-analysis
11 weeks ago by
mohammadhassanj
▴ 260
3
votes
12
replies
3.0k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 10 months ago by
Pegasus
▴ 100 • written 4.5 years ago by
mnazir
▴ 10
2
votes
12
replies
3.3k
views
WCGNA installation help
R
WGCNA
updated 7 weeks ago by
Ram
43k • written 4.8 years ago by
prekrish
• 0
2
votes
12
replies
1.6k
views
gatk Funcotator
vcf
Funcotator
gatk
9 months ago by
Saurabh
• 0
2
votes
12
replies
1.4k
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 8 months ago by
Nitin Narwade
★ 1.6k • written 8 months ago by
bioinformatics
▴ 40
5
votes
11
replies
945
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 7 months ago by
Ram
43k • written 7 months ago by
Chris
▴ 260
0
votes
11
replies
674
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 12 days ago by
barslmn
★ 2.1k • written 23 days ago by
avelarbio46
▴ 30
2
votes
11
replies
688
views
Reference Guided genome assembly
tabix
updated 4 weeks ago by
Michael
54k • written 5 weeks ago by
sainavyav22
• 0
4
votes
11
replies
543
views
Remove X in row name with only number
GSVA
updated 7 weeks ago by
Ram
43k • written 7 weeks ago by
Chris
▴ 260
0
votes
11
replies
2.2k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 9 months ago by
Ram
43k • written 4.9 years ago by
saumya.sharma1509
• 0
4
votes
11
replies
1.5k
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
updated 5 months ago by
Brian Bushnell
20k • written 7 months ago by
Y
• 0
2
votes
11
replies
956
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
3 months ago by
sil_bioinfo
▴ 40
2
votes
11
replies
5.1k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 10 weeks ago by
e.r.zakiev
▴ 170 • written 7.7 years ago by
CAnna
▴ 20
1
vote
11
replies
293
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 8 hours ago by
GenoMax
140k • written 14 hours ago by
Lila M
★ 1.2k
5
votes
11
replies
1.2k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 7 months ago by
cmdcolin
★ 3.7k • written 7 months ago by
pablo
▴ 300
0
votes
11
replies
1.6k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 9 months ago by
Ram
43k • written 5.2 years ago by
BioBaby
▴ 20
1
vote
11
replies
1.1k
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 6 months ago by
GenoMax
140k • written 7 months ago by
langziv
▴ 50
0
votes
11
replies
1.1k
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
6 months ago by
evmae
• 0
4
votes
11
replies
1.7k
views
PCA WITH PLINK
PLINK
updated 7 months ago by
Kevin Blighe
87k • written 7 months ago by
Michelle Guerra
• 0
2
votes
10
replies
3.1k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 6 months ago by
Raygozak
★ 1.4k • written 5.7 years ago by
kakukeshi
▴ 80
0
votes
10
replies
805
views
ONT Raw Read Sequencing Pipeline
remora
dorado
ONT
Basecall
9 weeks ago by
turcoa1
• 0
5
votes
10
replies
812
views
Error when viewing a bam file
samtools
updated 9 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
14
votes
10
replies
784
views
How to remove center population from seurat cluster
single-cell
3 months ago by
synat.keam
▴ 100
2
votes
10
replies
714
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 11 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
10
replies
780
views
Problem running scPred
scPred
scPredict
updated 15 days ago by
Ram
43k • written 12 weeks ago by
Nitin
• 0
1
vote
10
replies
3.0k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Kumar
▴ 120
8
votes
10
replies
2.0k
views
PyWGCNA
WGCNA
9 months ago by
yoshifumimiya
▴ 40
2
votes
10
replies
4.2k
views
Error encountered while running stattest from ballgown package
bioconductor
RNA-Seq
ballgown
stattest
updated 11 months ago by
Ram
43k • written 6.9 years ago by
lakhujanivijay
5.8k
1
vote
10
replies
1.1k
views
Coverage histogram query
Alignment
7 months ago by
prasundutta87
▴ 660
3
votes
10
replies
1.1k
views
STAR index not working
STAR
RNA-Seq
6 months ago by
camillab.
▴ 160
1
vote
10
replies
899
views
file conversion from gtf to gff3 for evidence modeler
gff3
stringtie
gtf
5 months ago by
rj.rezwan
• 0
1
vote
10
replies
1.1k
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 7 months ago by
Jeremy
▴ 880 • written 7 months ago by
jinyu
▴ 10
1
vote
10
replies
5.7k
views
which field has more scope Bioinformatics or Biomedical engineering at MS level???
biomedical
updated 11 months ago by
Ram
43k • written 7.6 years ago by
purpledora100
• 0
1
vote
10
replies
1.6k
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 6 months ago by
jeffhsu3
• 0 • written 8 months ago by
fra.silvestro
▴ 10
5
votes
10
replies
1.2k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
7 months ago by
alwayshope
▴ 40
1
vote
9
replies
554
views
Problem with ONT sequencing pipeline. Probably in the Samtools part
bam
samtools
ONT
updated 10 weeks ago by
GenoMax
140k • written 10 weeks ago by
Emilio
• 0
1
vote
9
replies
2.0k
views
kallisto bootstrap / condo installation problem
hfd5
kallisto
condo
updated 11 months ago by
dsull
★ 5.7k • written 11 months ago by
micecanfly
▴ 10
0
votes
9
replies
251
views
Low number of both surviving reads after trimming
trimmomatic
trimming
3 hours ago by
Jay
• 0
2
votes
9
replies
982
views
Read length for single -ended RNA seq data analysis
read-length
fastq
updated 8 months ago by
Ram
43k • written 8 months ago by
vinaya
• 0
2
votes
9
replies
1.1k
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
4 months ago by
ian.will
▴ 20
1
vote
9
replies
827
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
4 months ago by
i.sudbery
18k
4
votes
9
replies
1.1k
views
Snakemake issue with wrappers
Python
Snakemake
4 months ago by
Begonia_pavonina
▴ 140
0
votes
9
replies
1.4k
views
Samtools sam to bam error
samtools
updated 4 months ago by
Andrea
• 0 • written 23 months ago by
kb_93
▴ 10
3
votes
9
replies
735
views
Understanding this analysis pipeline
reads
updated 9 months ago by
Ram
43k • written 9 months ago by
artemchuki
• 0
1
vote
9
replies
440
views
miRNA alignment with Bowtie2
bowtie2
13 days ago by
Chironex
▴ 40
4
votes
9
replies
2.5k
views
Blast+ remote database names
blast
remote
databases
Blastplus
updated 8 months ago by
GenoMax
140k • written 2.2 years ago by
Komalharini
• 0
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 6 months ago by
svp
▴ 680 • written 6 months ago by
smrutimayipanda
▴ 20
6
votes
9
replies
1.9k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 10 months ago by
Ram
43k • written 14 months ago by
luzglongoria
▴ 50
0
votes
9
replies
834
views
fragments file generation via Sinto from CellRanger output
scATAC
alignment
scRNA
Sinto
10x
5 months ago by
ntsopoul
▴ 60
0
votes
9
replies
1.0k
views
grep multiple lines form file
shell-script
grep
updated 9 months ago by
Ram
43k • written 3.9 years ago by
harry
▴ 30
1,000 results • Page
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Answer: log2(TPM+1)
Comment: Error in openning FastQC
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Answer: 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: 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…
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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…
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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?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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