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1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
15
votes
15
replies
23k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 16 days ago by
Ram
36k • written 6.6 years ago by
dam4l
▴ 180
10
votes
5
replies
5.7k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 7 days ago by
Ram
36k • written 7.0 years ago by
seta
★ 1.7k
9
votes
9
replies
537
views
Which hg38 file?
reference
hg38
NCBI
updated 5 days ago by
appropiate
▴ 50 • written 17 days ago by
amy__
▴ 30
9
votes
4
replies
1.8k
views
[Code] Converte fasta/fa files to fastq
perl
fastq
sed
fasta
updated 6 days ago by
Ram
36k • written 6.8 years ago by
Shicheng Guo
★ 9.1k
9
votes
1
reply
3.0k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 8 days ago by
Ram
36k • written 7.2 years ago by
Niek De Klein
★ 2.6k
8
votes
11
replies
700
views
using STAR instead of HISAT2
STAR
updated 20 days ago by
Ram
36k • written 22 days ago by
Chris
• 0
8
votes
3
replies
4.7k
views
Bioinformatics project for a beginner
projects
updated 27 days ago by
Ram
36k • written 6.7 years ago by
dharshank.1096
▴ 30
8
votes
9
replies
2.4k
views
error in rstudio
csv
matrix
rstudio
updated 26 days ago by
Ram
36k • written 7.0 years ago by
Angel
★ 4.1k
7
votes
4
replies
340
views
Error: missing values and NaN's not allowed if 'na.rm' is FALSE
Genome
Software
27 days ago by
sunnykevin97
▴ 970
7
votes
5
replies
3.5k
views
Trinity de novo transcript assembly too many transcripts
RNA-Seq
Assembly
updated 16 days ago by
Ram
36k • written 7.2 years ago by
Mehmet
▴ 780
6
votes
7
replies
5.6k
views
best alignment tool for Ion Torrent data
chloroplast
genome
iontorrent
updated 8 days ago by
Ram
36k • written 6.7 years ago by
Ann
★ 2.3k
6
votes
4
replies
2.3k
views
Trouble renaming output files after running PHYLIP programs from a BASH script
PHYLIP
sequence
software-error
updated 14 days ago by
Ram
36k • written 6.7 years ago by
sviatoslav.kendall
▴ 830
6
votes
14
replies
2.3k
views
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
RNA-Seq
sequence
cufflinks
new isoform in rnaseq
updated 29 days ago by
Ram
36k • written 6.5 years ago by
fta.mirzadeh
• 0
6
votes
5
replies
1.6k
views
the gene_id column is different for each sample when counting fpkm in galaxy cufflinks
RNA-Seq
galaxy
cufflinks
fpkm
updated 27 days ago by
Ram
36k • written 6.7 years ago by
Angel
★ 4.1k
6
votes
13
replies
5.7k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq
edgeR
DESeq2
updated 8 days ago by
Ram
36k • written 6.7 years ago by
ilyco
▴ 60
6
votes
2
replies
3.9k
views
Adding header to VCF and combine VCF
vcf
updated 27 days ago by
Ram
36k • written 6.8 years ago by
basalganglia
▴ 40
5
votes
7
replies
2.6k
views
Merging bam files
bam
merge
updated 9 days ago by
Ram
36k • written 6.7 years ago by
jyu429
▴ 120
5
votes
4
replies
7.3k
views
GFF3 to GTF conversion - 9th column
gtf
NCBI
gff3
featureCounts
updated 19 days ago by
Ram
36k • written 6.6 years ago by
mrodrigues.fernanda
▴ 50
5
votes
14
replies
825
views
Removing sequences that contain deletion mutations in them from a fasta file (with python)
python
17 days ago by
Mustafa
▴ 10
5
votes
3
replies
267
views
A question about BED file and finding mutation in vcf file
VCF
BED
20 days ago by
Zahra
▴ 60
5
votes
3
replies
2.1k
views
Parsing error with Provean : Someone else ?
Provean
software-error
updated 7 days ago by
tony
• 0 • written 7.9 years ago by
jsgounot
▴ 170
5
votes
0
replies
3.5k
views
Interpreting dispersion plots in RNAseq analysis
RNA-Seq
dispersion
updated 8 days ago by
Ram
36k • written 6.7 years ago by
Shellfishgene
▴ 60
5
votes
22
replies
5.9k
views
SVM for classified gene expression data
R
svm
microarray
updated 19 days ago by
Ram
36k • written 6.6 years ago by
Shaurya Jauhari
▴ 50
5
votes
5
replies
1.8k
views
Truncating BAM Files
bam
sam
RNA-Seq
samtools
pysam
updated 6 days ago by
Ram
36k • written 6.7 years ago by
JameB11
▴ 10
5
votes
1
reply
4.9k
views
Generating Gencode TSS file
gencode
tss
updated 8 days ago by
Ram
36k • written 6.7 years ago by
dally
▴ 210
5
votes
2
replies
2.0k
views
Assemble fully overlapping reads into contigs that may have several clones
assembly
updated 16 days ago by
Ram
36k • written 6.6 years ago by
Iayork
▴ 10
5
votes
5
replies
1.4k
views
How to determine whether a contig is sex-linked
sequence
updated 8 days ago by
Ram
36k • written 6.7 years ago by
ecophylic
▴ 20
5
votes
4
replies
5.3k
views
HGNC gene symbols
gene
ensembl
hgnc
updated 15 days ago by
Ram
36k • written 6.6 years ago by
hirak.sarkar
▴ 20
5
votes
0
replies
1.8k
views
Result difference between blastall -p blastp (legacy blast) and blastp -task blastp (blast+)
software-error
blast
updated 9 days ago by
Ram
36k • written 6.7 years ago by
ahsan.chattha15
▴ 50
5
votes
5
replies
1.4k
views
I have a GRN, now what?
GRN
network-analysis
updated 16 days ago by
Ram
36k • written 6.6 years ago by
guiu
▴ 60
5
votes
3
replies
3.1k
views
Homozygous SNP and Heterozygous SNP
SNP
updated 9 days ago by
Ram
36k • written 6.7 years ago by
wanghaho9797
• 0
5
votes
11
replies
5.9k
views
Error while running miso
RNA-Seq
splicing
updated 16 days ago by
Ram
36k • written 7.0 years ago by
priyankamaripuri
▴ 40
4
votes
5
replies
271
views
Reference counts for RNA-seq
expression
rna
rna-seq
tpm
transcripts
updated 6 days ago by
ATpoint
64k • written 8 days ago by
syntax
▴ 70
4
votes
11
replies
506
views
Running STAR
STAR
15 days ago by
Chris
• 0
4
votes
3
replies
3.2k
views
Very few DE genes from Limma analysis of RNA-seq data: design matrix problem?
contrasts
Limma
RNA-Seq
R
design-matrix
updated 26 days ago by
Ram
36k • written 6.5 years ago by
Michelle M.
▴ 60
4
votes
4
replies
1.6k
views
is Hapmap or 1000 genome VCF data is from diseased or healthy one
RNA-Seq
vcf
purifying-selection
updated 2 days ago by
Ram
36k • written 6.9 years ago by
Being Bioinformatician
▴ 230
4
votes
2
replies
1.5k
views
Length of RNAseq reads
RNA-Seq
miRNA
updated 15 days ago by
Ram
36k • written 6.6 years ago by
silas008
▴ 150
4
votes
6
replies
349
views
About normalization of the datasets from Harmonized TCGA data
profiling
data
normalisation
transcript
protein
7 days ago by
qiz218591
▴ 10
4
votes
2
replies
2.4k
views
Cufflinks bias correction
RNA-Seq
updated 6 days ago by
Ram
36k • written 6.9 years ago by
Xin
▴ 70
4
votes
4
replies
2.4k
views
RNA-Seq counts for all genes?
RNA-Seq
updated 16 days ago by
Ram
36k • written 6.6 years ago by
ra381
▴ 10
4
votes
1
reply
3.0k
views
How to calculate 4DTv distance (D4DTv) that stands for fourfold synonymous third-codon transversion ?
gene
codon
updated 13 days ago by
Ram
36k • written 6.7 years ago by
Michel Edwar
▴ 70
4
votes
4
replies
1.8k
views
gap filling solution
sequence
updated 19 days ago by
Ram
36k • written 6.6 years ago by
Bulbul Ahmed
▴ 20
4
votes
2
replies
1.9k
views
Retrieve a large dataset of biological sequences with Perl
perl
ncbi
sequence
updated 27 days ago by
Ram
36k • written 7.1 years ago by
Helder Gomes
▴ 10
4
votes
6
replies
7.7k
views
Spades assembler output
Assembly
updated 19 days ago by
Ram
36k • written 6.6 years ago by
elbecerrasoto
▴ 30
4
votes
3
replies
238
views
Difference in sashimi plot between single-cell versus bulk RNA-seq data
pysashimi
12 days ago by
tien
▴ 10
4
votes
10
replies
757
views
downloading and running tidyverse package in R
seq
analysis
tidyverse
rna
27 days ago by
bioinformatics
▴ 10
4
votes
18
replies
3.0k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 9 days ago by
Ram
36k • written 6.7 years ago by
Joel TM
▴ 60
3
votes
2
replies
190
views
Mapping GeneSymbol plus cDNA position to a Chr:Position ... without transcript ID.
annotation
splice
site
transcript
build
1 day ago by
Vincent Laufer
★ 2.2k
3
votes
7
replies
1.3k
views
Why blast doesn't cache previous queries?
blast
updated 8 days ago by
Ram
36k • written 6.7 years ago by
roy.granit
▴ 880
3
votes
3
replies
3.9k
views
Configuring sleuth for log2FC - What are the dangers?
sleuth
RNA-Seq
updated 15 days ago by
lessismore
★ 1.2k • written 4.5 years ago by
Lorenz Becker
▴ 20
1,000 results • Page
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Recent Votes
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VN in ` VN: ` should have a value. The htsjdk library _requires_ a value here: https://github.com/gkno/picard/blob/ffb68b5183efdaa561…
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by
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• 0
May I chat with you somewhere for more detail?
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Commenting to update: it seems that this issue is solved not at the level of the program, but at the level of the command line. `snakemake …
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Comment: Gene-based and transcriptome-based profiling
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119k
It may be a case of semantics. When arrays were popular in early 2000s, people used the term "gene-based profiling". Both cases one is look…
Comment: Changing the x-axis in ggseqlogo in R
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36k
I've moved the comment to an answer. Please accept it to mark the post as solved.
Comment: Changing the x-axis in ggseqlogo in R
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margo
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Thank you! That works!
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9.4k
Untested but adding `+ scale_x_continuous(breaks=1:21, labels=-10:10)` to the returned ggplot2 object should work.
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Thank you so much for detailed answer! I am not confused about transcriptome-base profiling because I think it is RNA-Seq analysis. I only …
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Its not that we don't know which transcripts are poly-adenylated and which arn't - its just that that information is not encoded in the gen…
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