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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
11
votes
7
replies
14k
views
6 follow
How to extract specific rows based on row number from a file
shell
updated 4 days ago by
Ram
38k • written 4.9 years ago by
vinayjrao
▴ 220
11
votes
8
replies
665
views
How to perform synteny alignments and plots only with a gene?
Comparative
Evolution
Alignment
Synteny
Genomics
5 days ago by
Rafael Soler
★ 1.1k
11
votes
8
replies
2.0k
views
Download Brachypodium Distachyon Genome
genome
updated 2 days ago by
Ram
38k • written 11.7 years ago by
Sara
▴ 130
11
votes
7
replies
9.6k
views
7 follow
Extract reads from bam/sam files using read id
fastq
bam
samtools
alignment
updated 4 days ago by
Ram
38k • written 7.4 years ago by
Chirag Parsania
★ 2.0k
11
votes
9
replies
5.0k
views
Does multiIntersectBed works with -u and -f parameter?
bed
sequencing
bedtools
intersect
updated 4 days ago by
Ram
38k • written 8.1 years ago by
ivivek_ngs
★ 5.2k
11
votes
6
replies
5.5k
views
Where Can I Download Nucleotide Sequences Of Bacterial Genes?
bacteria
gene
updated 2 days ago by
Ram
38k • written 11.1 years ago by
Tianyang Li
▴ 500
11
votes
11
replies
2.9k
views
8 follow
Forum:
Best open source genome browser in 2020
genome-browser
genomics
updated 5 days ago by
Ram
38k • written 2.4 years ago by
mrmrwinter
▴ 30
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 5 days ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
10
votes
11
replies
3.2k
views
Forum:
48 Replicate RNA-Seq Study Points to Replicates Needed for DGE
RNA-seq
differential-gene-expression
updated 5 days ago by
Ram
38k • written 7.9 years ago by
support
▴ 640
10
votes
7
replies
4.3k
views
Vcf File With Variants And Genotypes For A "Single Individual"
vcf
snp
updated 2 days ago by
Ram
38k • written 10.6 years ago by
Nasrin
▴ 30
10
votes
5
replies
4.5k
views
How Do I Download All Full-Text Papers From A Dspace Repository?
DSpace
papers
updated 2 days ago by
Ram
38k • written 12.6 years ago by
Lars Juhl Jensen
11k
10
votes
10
replies
29k
views
7 follow
How To Download .Gbk Files From Ncbi Website
ncbi
genbank
updated 3 days ago by
Ram
38k • written 11.3 years ago by
Arun
• 0
10
votes
5
replies
912
views
Merging Bed files with depth information
bed
bedops
bedtools
updated 5 days ago by
Ram
38k • written 16 months ago by
asdasd
▴ 20
10
votes
5
replies
2.3k
views
Forum:
What are your "model" examples for bioinformatics programming?
github
RNA-Seq
updated 2 days ago by
Ram
38k • written 7.7 years ago by
Dan D
7.4k
10
votes
6
replies
2.3k
views
Easiest way to download all Enterobacteria
ncbi
genome
refseq
updated 2 days ago by
Ram
38k • written 5.1 years ago by
Joe
20k
10
votes
7
replies
28k
views
How To Batch Download Journal Papers (Pdf)?
papers
updated 2 days ago by
Ram
38k • written 10.7 years ago by
Hranjeev
★ 1.5k
10
votes
9
replies
1.0k
views
Merging two files based on a particular column
r
updated 4 days ago by
Ram
38k • written 3.5 years ago by
mohammedtoufiq91
▴ 210
10
votes
5
replies
3.5k
views
How To Get A List Of All Human Genes Above A Certain Length
human
gene
updated 2 days ago by
Ram
38k • written 9.9 years ago by
Whetting
★ 1.6k
10
votes
7
replies
9.5k
views
BedTools IntersectBed resulting in Segmentation Fault with BedFile
intersectbed
vcf
bed
bedtools
updated 4 days ago by
Ram
38k • written 8.3 years ago by
ali
• 0
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 4 days ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
10
votes
18
replies
14k
views
8 follow
Please help with removing spaces from fasta file
fasta
updated 4 days ago by
Ram
38k • written 7.2 years ago by
seta
★ 1.8k
10
votes
4
replies
5.1k
views
pearson correlation or Euclidean distance for clustering?
gene-expression
updated 3 days ago by
Ram
38k • written 2.5 years ago by
mrashad
▴ 60
10
votes
8
replies
8.8k
views
10 follow
How to extract fasta sequences from assembled transcripts generated by Stringtie
fasta
gtf
stringtie
updated 4 days ago by
Ram
38k • written 5.9 years ago by
seta
★ 1.8k
10
votes
22
replies
6.0k
views
12 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 4 days ago by
Ram
38k • written 14 months ago by
ConvolutedGenome
▴ 10
10
votes
7
replies
2.6k
views
Job:
Scientific Programmer at DSM Biotechnology Center, Delft, The Netherlands
C-sharp
scientific-programming
Java
updated 3 days ago by
Ram
38k • written 3.9 years ago by
evelien.vlap
▴ 50
9
votes
6
replies
472
views
6 follow
split fasta file to train deep learning model
fasta
split
bash
R
updated 6 days ago by
shenwei356
7.9k • written 7 days ago by
pinheirofabiano
▴ 10
9
votes
4
replies
4.0k
views
How To Get All Proteins Smaller Than 200 Amino Acids Out Of Ncbi Nr Database?
ncbi
fasta
protein
updated 2 days ago by
Ram
38k • written 11.0 years ago by
Niek De Klein
★ 2.6k
9
votes
5
replies
5.2k
views
Forum:
Can I switch back to wet lab in phd after doing a master in bioinformatics?
biology
wet-lab
phd
updated 5 days ago by
Ram
38k • written 7.9 years ago by
blueearth205
▴ 10
9
votes
4
replies
315
views
Snakemake, snake files
Snakemake
updated 6 days ago by
Ram
38k • written 4 months ago by
beginner123
• 0
9
votes
5
replies
1.0k
views
Kallisto in snakePipes instead of salmon
salmon
snakePipes
updated 3 days ago by
Ram
38k • written 3.1 years ago by
arunprasanna83
▴ 60
9
votes
7
replies
6.6k
views
6 follow
Multiple whole genome alignment
alignment
Assembly
sequencing
updated 5 days ago by
Ram
38k • written 7.8 years ago by
robjohn7000
▴ 110
9
votes
14
replies
1.0k
views
6 follow
Downloading a huge amount of Fastq files
fastq
updated 3 days ago by
Ram
38k • written 9 months ago by
davidmaimoun
▴ 50
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 4 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
10
replies
5.0k
views
Error parsing SAM header. @RG line missing SM tag
alignment
samtools
BAM
updated 4 days ago by
Ram
38k • written 5.4 years ago by
kwangchol.mun
▴ 10
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 4 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
12
replies
28k
views
6 follow
How To Download Gene Sequences From Ncbi Gene
ncbi
fasta
gene
updated 2 days ago by
Ram
38k • written 11.3 years ago by
Pierre
▴ 20
9
votes
7
replies
900
views
How to work out coverage (100X) of WES using exome bed file?
bed
WES
coverage
updated 5 days ago by
Ram
38k • written 11 months ago by
amy__
▴ 50
9
votes
8
replies
16k
views
Key Passphrase For Ascp File Transfer (Ebi, Ncbi)
ncbi
ascp
aspera
updated 4 days ago by
Ram
38k • written 9.1 years ago by
Gangcai
▴ 230
9
votes
3
replies
1.7k
views
Tool:
SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta
sequences
java
updated 5 days ago by
Ram
38k • written 3.3 years ago by
Hugo
▴ 370
9
votes
8
replies
3.2k
views
6 follow
Tool:
NCBI-SRA File Downloader
NCBI
sra
sequence
updated 2 days ago by
Ram
38k • written 7.6 years ago by
sanjay.deshpande
▴ 50
8
votes
14
replies
887
views
"transcript reads were aligned to the RefSeq transcriptome (downloaded March 2013) using Tophat" was done by orginal author.Please help me to get tha…
RNA-Seq
RefSeq
updated 3 days ago by
Ram
38k • written 12 months ago by
Pari
• 0
8
votes
10
replies
4.3k
views
Calculating inner mate distance for paired reads
alignment
bam
updated 4 days ago by
Ram
38k • written 6.4 years ago by
dgimode
▴ 70
8
votes
6
replies
17k
views
How Can I Download Or Get A Pathway List From Kegg
kegg
pathway
updated 2 days ago by
Ram
38k • written 9.9 years ago by
rezwan.02
▴ 60
8
votes
6
replies
3.3k
views
Problem To Convert Pdb Text File To Jmol Jar File
pdb
java
updated 3 days ago by
Ram
38k • written 12.7 years ago by
Hazelin
▴ 100
8
votes
3
replies
1.7k
views
HISAT output SAM file incorrect (only contains 3 columns of data)
HISAT
SAM
updated 4 days ago by
Ram
38k • written 5.0 years ago by
emcc
▴ 30
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 5 days ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
8
votes
3
replies
1.6k
views
How to study gene expression network?
network
gene-expression
updated 5 days ago by
Ram
38k • written 4.1 years ago by
afli
▴ 190
8
votes
5
replies
4.7k
views
How can I make a BED file from a VCF file?
BED
Bedtools
updated 4 days ago by
Ram
38k • written 2.9 years ago by
VictoriaP
▴ 20
8
votes
12
replies
8.4k
views
7 follow
How to make sure there is no duplicate sequence in a fasta file?
fasta
sequence
updated 4 days ago by
Ram
38k • written 7.5 years ago by
seta
★ 1.8k
8
votes
6
replies
434
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 3 days ago by
Ram
38k • written 12 days ago by
O.rka
▴ 650
1,000 results • Page
2 of 20
Recent Votes
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Answer: Somatic truth set
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▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39
by
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• 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
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Perfect answer, thanks Ben!
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Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq?
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Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq
by
GenoMax
127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq
by
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▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts?
by
dsull
★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank
by
GenoMax
127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq
by
GenoMax
127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq
by
ATpoint
70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank
by
Mensur Dlakic
★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold
by
ATpoint
70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat
by
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★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq?
by
Ming Tommy Tang
★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
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