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387 results • Page
2 of 8
Sort: replies
Rank
Views
Votes
Replies
4
votes
8
replies
3.6k
views
downloading bam files of phase 3 of 1000 genomes project
1000genomes
bam
updated 21 hours ago by
Ram
38k • written 4.9 years ago by
Ana
▴ 200
9
votes
8
replies
16k
views
Key Passphrase For Ascp File Transfer (Ebi, Ncbi)
ncbi
ascp
aspera
updated 21 hours ago by
Ram
38k • written 9.1 years ago by
Gangcai
▴ 230
0
votes
8
replies
1.9k
views
How to extract mutation signatures from a merged vcf file with multiple groups of samples
vcf
mutation-signature
updated 18 hours ago by
Ram
38k • written 3.7 years ago by
sagardesai91
▴ 50
3
votes
8
replies
1.2k
views
Best way to generate a bed file
bed
updated 19 hours ago by
Ram
38k • written 5.6 years ago by
elisheva
▴ 120
3
votes
8
replies
721
views
Merging .fq files per sample using a big loop - BASH?
fastq
bash
genomics
updated 18 hours ago by
Ram
38k • written 2.1 years ago by
giulia.trauzzi
▴ 10
0
votes
8
replies
2.4k
views
Split paired-end reads BAM file into Forward and Reverse Strands
RNA-seq
BAM
updated 20 hours ago by
Ram
38k • written 2.3 years ago by
GA
• 0
2
votes
8
replies
1.5k
views
Genomic coordinates from GENCODE annotation file
GENCODE
genomic-coordinates
GTF
updated 21 hours ago by
Ram
38k • written 4.4 years ago by
seta
★ 1.8k
10
votes
8
replies
8.8k
views
10 follow
How to extract fasta sequences from assembled transcripts generated by Stringtie
fasta
gtf
stringtie
updated 21 hours ago by
Ram
38k • written 5.9 years ago by
seta
★ 1.8k
11
votes
7
replies
9.6k
views
7 follow
Extract reads from bam/sam files using read id
fastq
bam
samtools
alignment
updated 19 hours ago by
Ram
38k • written 7.4 years ago by
Chirag Parsania
★ 2.0k
3
votes
7
replies
2.7k
views
Rmoving - from sequence data fasta file
fasta
aliview
updated 20 hours ago by
Ram
38k • written 5.0 years ago by
James
▴ 20
0
votes
7
replies
1.5k
views
File format for HGMD pro file flat
variant-analysis
HGMD
annovar
updated 19 hours ago by
Ram
38k • written 4.2 years ago by
NB
▴ 960
2
votes
7
replies
1.3k
views
6 follow
Extract N amino acids from fasta file
fasta
sequence
updated 20 hours ago by
Ram
38k • written 3.3 years ago by
martha.chapa.mc18
• 0
4
votes
7
replies
2.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 22 hours ago by
Ram
38k • written 20 months ago by
mathavanbioinfo
▴ 70
7
votes
7
replies
266
views
Run nextflow sections sequentially
nextflow
updated 3 hours ago by
colindaven
4.6k • written 19 hours ago by
Raygozak
★ 1.4k
1
vote
7
replies
219
views
How to find promoter sequence of a gene?
promoter
34 minutes ago by
sunyeping
▴ 40
11
votes
7
replies
14k
views
6 follow
How to extract specific rows based on row number from a file
shell
updated 18 hours ago by
Ram
38k • written 4.9 years ago by
vinayjrao
▴ 220
7
votes
7
replies
1.1k
views
Is there a way to produce/convert nhmmer output to a bed file?
bed
nhmmer
updated 19 hours ago by
Ram
38k • written 2.4 years ago by
jamie.pike
▴ 80
1
vote
7
replies
855
views
Splitting BED file by technical replicate or extract all unique barcodes
BED
updated 19 hours ago by
Ram
38k • written 2.6 years ago by
summer_researcher
• 0
10
votes
7
replies
9.4k
views
BedTools IntersectBed resulting in Segmentation Fault with BedFile
intersectbed
vcf
bed
bedtools
updated 19 hours ago by
Ram
38k • written 8.3 years ago by
ali
• 0
7
votes
7
replies
3.3k
views
How to sort chromosome name in bed file
bed
updated 19 hours ago by
Ram
38k • written 6.7 years ago by
raya.girish
▴ 30
1
vote
7
replies
3.2k
views
Duplicate SAMSequenceDictionary in SAM file - how to modify SAM header?
sam
bwa
SequenceDictionary
updated 20 hours ago by
Ram
38k • written 4.7 years ago by
kat
▴ 40
2
votes
6
replies
434
views
Saving file as .vcf
NGS
Variant
VCF
updated 20 hours ago by
Ram
38k • written 10 months ago by
Maryam
▴ 10
1
vote
6
replies
1.0k
views
gff file
GFF
UNIPRTOT
updated 23 hours ago by
Ram
38k • written 18 months ago by
devhimd
▴ 10
3
votes
6
replies
2.2k
views
bwa and bowtie2 bamfile format
bam
bowtie2
bwa
updated 20 hours ago by
Ram
38k • written 6.4 years ago by
nkinney06
▴ 90
3
votes
6
replies
4.7k
views
Please help me with pyfasta
fasta
pyfasta
updated 20 hours ago by
Ram
38k • written 7.0 years ago by
seta
★ 1.8k
1
vote
6
replies
883
views
extract uniprot id from pdb header file
uniprot
pdb
updated 23 hours ago by
Ram
38k • written 17 months ago by
devhimd
▴ 10
2
votes
6
replies
735
views
How to work with .man files?
ncbi
transcriptome
updated 20 hours ago by
Ram
38k • written 9 months ago by
Lalit
▴ 10
4
votes
6
replies
1.8k
views
Michigan imputation server error
TOPMed
VCF
updated 21 hours ago by
Ram
38k • written 2.7 years ago by
AR
• 0
6
votes
6
replies
1.7k
views
Coverage per gene
gene-coverage
bed
bedtools
updated 19 hours ago by
Ram
38k • written 2.9 years ago by
gubrins
▴ 260
1
vote
6
replies
5.0k
views
Problem viewing BAM files in IGV - samtools sort error?
alignment
updated 23 hours ago by
Ram
38k • written 7.7 years ago by
harriet.hunt897
▴ 10
6
votes
6
replies
1.8k
views
Which SNPs fall within genes and what's their description?
bed
gff
snp
gene
updated 19 hours ago by
Ram
38k • written 6.1 years ago by
paulotyama
• 0
3
votes
6
replies
973
views
Ensembl encoding problem
Ensembl
encoding
updated 22 hours ago by
Ram
38k • written 20 months ago by
giammafer
▴ 20
0
votes
6
replies
231
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 3 hours ago by
GenoMax
127k • written 19 hours ago by
Human
• 0
0
votes
6
replies
254
views
Mapping paired end reads with ngm and samtools, using prefixes and suffixes for creating vcf eventually
ngm
sam
samtools
updated 17 hours ago by
Ram
38k • written 1 day ago by
Human
• 0
2
votes
6
replies
1.3k
views
TSS of protein coding genes
TSS
protein coding genes
ucsc
updated 3 hours ago by
ConvolutedGenome
▴ 10 • written 2.6 years ago by
arsala521
▴ 10
0
votes
6
replies
1.1k
views
Raw data for chromosome 21
WCS
bam
sequencing
updated 20 hours ago by
Ram
38k • written 4.0 years ago by
tamara912
• 0
0
votes
6
replies
943
views
6 follow
Supplementary alignments in BAM-file
galaxy
Samtools
bam
updated 20 hours ago by
Ram
38k • written 8 months ago by
mokbel73
• 0
1
vote
6
replies
857
views
Secuence length in bed file
bed
python
sequence
updated 19 hours ago by
Ram
38k • written 2.4 years ago by
lsudupe
▴ 10
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 19 hours ago by
Ram
38k • written 16 months ago by
Nikhil
▴ 10
1
vote
6
replies
3.7k
views
6 follow
How to run ABSOLUTE with WGS bam files ?
CNA
next-gen
ABSOLUTE
bam
updated 20 hours ago by
Ram
38k • written 6.8 years ago by
subhajit06
▴ 110
6
votes
6
replies
810
views
What is a FASTA format file ?
Sequence
NCBI
FASTA
Genome
updated 21 hours ago by
Ram
38k • written 22 months ago by
Student
▴ 30
2
votes
6
replies
1.1k
views
Draw coverage plot from bed file
bed
deeptools
coverage
updated 19 hours ago by
Ram
38k • written 3.6 years ago by
ben.kunfang
▴ 30
0
votes
5
replies
650
views
BED files usage a beginners query!
sam
bam
variant-calling
ngs
bed
updated 20 hours ago by
Ram
38k • written 9 months ago by
mital.bhatt14
• 0
4
votes
5
replies
1.1k
views
What are "unused reference sequences" in a bam file?
sam
bam
samtools
updated 20 hours ago by
Ram
38k • written 3.6 years ago by
anniejeanforster
▴ 10
1
vote
5
replies
452
views
multivariate Cox analysis bladder cancer
bladder-cancer
statistics
survival-analysis
updated 21 hours ago by
Ram
38k • written 6 months ago by
Nobody
▴ 30
32
votes
5
replies
5.2k
views
Forum:
ipython notebooks on bioinformatics and genomics
python
updated 23 hours ago by
Ram
38k • written 7.7 years ago by
Pappu
★ 2.1k
0
votes
5
replies
945
views
Problem with normalization by bcftools
vcf
bcftools
samtools
updated 21 hours ago by
Ram
38k • written 2.9 years ago by
Negin
▴ 20
0
votes
5
replies
831
views
Problems with consensus fasta
bed
bcftools
samtools
updated 19 hours ago by
Ram
38k • written 15 months ago by
Giulia.cosenza
▴ 80
3
votes
5
replies
6.6k
views
Problems with MAP/PED files manipulation
GWAS
SNP
PED
MAP
PLINK
updated 21 hours ago by
Ram
38k • written 8.6 years ago by
Cindy Chan
▴ 20
2
votes
5
replies
1.6k
views
Expanding Genomic Coordinates Using Bedtools
bed
bedtools
updated 19 hours ago by
Ram
38k • written 4.8 years ago by
gtasource
▴ 60
387 results • Page
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Recent Votes
Comment: TSV with multi-allelic sites to VCF
Comment: How to find promoter sequence of a gene?
Comment: What means this Error when running a script in python??
Comment: What means this Error when running a script in python??
Comment: Run nextflow sections sequentially
Answer: Differences between BioMart and Ensembl site
Answer: Differences between BioMart and Ensembl site
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Comment: What means this Error when running a script in python??
by
Antonia
• 0
Thank you Pierre! It wasn't clear for me at all lol Trully thank you
Answer: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
Thank you all for the help! To do the ChIP-seq, how many cells are needed? I am working on antigen-specific T cells in tissues, usually,…
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by
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in "configs/config_main.yaml", line 29, column 1 could not find expected ':' the message is quite clear to me : There is missing …
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I try to answer this question. Based on the Conditional Likelihood defined in https://rss.onlinelibrary.wiley.com/doi/epdf/10.1111/j.2517-6…
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Hi, You can use [NCBI Datasets][1] to retrieve gene information in JSON format. Using the gene id you used as an example, you can do thi…
Comment: How to find promoter sequence of a gene?
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Trivas
▴ 690
You can use the UCSC genome browser to get the the sequence of X bases upstream of a gene, then use tools in MEME-suite/JASPAR to look for …
Comment: How to find promoter sequence of a gene?
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Hello Jeo, We found that Jun/fos are highly expressed in RNAseq. But to map reads mapping to regions upstream of genes, do you mean ATAC…
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Is there have any papers to support these? Will you share some reporters?
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Thank You Sir for your reply.
Comment: Does it possible to know what are the adjacent genes up to 1000bp upstream and
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Thank you for your reply...
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Thanks! I would suggest adding a small explanation/note, probably in the RefSeq column tooltip.
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3.4k
Please describe in more detail what kind of input you have and which organism you are working with. As a rule of thumb, everything betwee…
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Yes, both are GRCh37.p13. [This is the link to the Biomart query][1] (you have to click Results), but I don't know how long the link will w…
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Hi jpuntomarcos, The transcript table you have observed will only show you a single RefSeq transcript that is mapped per Ensembl transcr…
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There have always been differences in web based results from NCBI and what you may get from command line tools. In this case if the data co…
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